A3

Accurate, Adaptable, and Accessible Error Metrics for Predictive Models

Found **13202** packages.

A3

Accurate, Adaptable, and Accessible Error Metrics for Predictive Models

a4

Automated Affymetrix Array Analysis Umbrella Package

a4Base

Automated Affymetrix Array Analysis Base Package

a4Classif

Automated Affymetrix Array Analysis Classification Package

a4Core

Automated Affymetrix Array Analysis Core Package

a4Core

Automated Affymetrix Array Analysis Core Package

a4Preproc

Automated Affymetrix Array Analysis Preprocessing Package

a4Reporting

Automated Affymetrix Array Analysis Reporting Package

a4Reporting

Automated Affymetrix Array Analysis Reporting Package

ABAEnrichment

Gene expression enrichment in human brain regions

ABarray

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

abbyyR

Access to Abbyy Optical Character Recognition (OCR) API

abc

Tools for Approximate Bayesian Computation (ABC)

ABCanalysis

Computed ABC Analysis

abc.data

Data Only: Tools for Approximate Bayesian Computation (ABC)

abcdeFBA

ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.

ABCoptim

Implementation of Artificial Bee Colony (ABC) Optimization

ABCp2

Approximate Bayesian Computational Model for Estimating P2

ABC.RAP

Array Based CpG Region Analysis Pipeline

abcrf

Approximate Bayesian Computation via Random Forests

abctools

Tools for ABC Analyses

abd

The Analysis of Biological Data

abd

The Analysis of Biological Data

abf2

Load Gap-Free Axon ABF2 Files

ABHgenotypeR

Easy Visualization of ABH Genotypes

abind

Combine Multidimensional Arrays

abind

Combine Multidimensional Arrays

abjutils

Useful Tools for Jurimetrical Analysis Used by the Brazilian Jurimetrics Association

abmi

Data Processing and Analysis for the Alberta Biodiversity Monitoring Institute

abmiOld

Data Processing and Analysis for the Alberta Biodiversity Monitoring Institute

abn

Modelling Multivariate Data with Additive Bayesian Networks

abodOutlier

Angle-Based Outlier Detection

abrem

Abernethy Reliability Methods

abremDebias

Maximum Likelihood Estimation Models with Bias Adjustment Options for Reliability Analysis

abremout

Output functions for the Abernethy Reliability Methods package (abrem), including plotting.

abremPivotals

Linear Rank Regression Models with Pivotal Monte Carlo Methods for Reliability Analysis

AbsFilterGSEA

Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering

AbSim

Time Resolved Simulations of Antibody Repertoires

ABSSeq

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

abundant

High-Dimensional Principal Fitted Components and Abundant Regression

ACA

Abrupt Change-Point or Aberration Detection in Point Series

acc

Exploring Accelerometer Data

accelerometry

Functions for Processing Minute-to-Minute Accelerometer Data

accelerometry

Functions for Processing Minute-to-Minute Accelerometer Data

accelmissing

Missing Value Imputation for Accelerometer Data

AcceptABEL

A package for controlling false positives rate in GWAS by estimating local inflation factor

AcceptanceSampling

Creation and Evaluation of Acceptance Sampling Plans

ACCLMA

ACC & LMA Graph Plotting

accrual

Bayesian Accrual Prediction

accrued

Data Quality Visualization Tools for Partially Accruing Data

ACD

Categorical data analysis with complete or missing responses

acde

Artificial Components Detection of Differentially Expressed Genes

ACDm

Tools for Autoregressive Conditional Duration Models

acebayes

Optimal Bayesian Experimental Design using the ACE Algorithm

acepack

ACE and AVAS for Selecting Multiple Regression Transformations

ACEt

Estimating Dynamic Heritability and Twin Model Comparison

ACEt

Estimating Dynamic Heritability and Twin Model Comparison

aCGH

Classes and functions for Array Comparative Genomic Hybridization data.

acid

Analysing Conditional Income Distributions

acm4r

Align-and-Count Method comparisons of RFLP data

ACME

Algorithms for Calculating Microarray Enrichment (ACME)

acmeR

Implements ACME Estimator of Bird and Bat Mortality by Wind Turbines

ACNE

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

acnr

Annotated Copy-Number Regions

acnr

Annotated Copy-Number Regions

acopula

Modelling dependence with multivariate Archimax (or any user-defined continuous) copulas.

acp

Autoregressive Conditional Poisson

aCRM

Convenience functions for analytical Customer Relationship Management

AcrossTic

A Cost-Minimal Regular Spanning Subgraph with TreeClust

acrt

Autocorrelation Robust Testing

acs

Download, Manipulate, and Present American Community Survey and Decennial Data from the US Census

ACSNMineR

Gene Enrichment Analysis from ACSN Maps or GMT Files

acss

Algorithmic Complexity for Short Strings

acss.data

Data Only: Algorithmic Complexity of Short Strings (Computed via Coding Theorem Method)

ACSWR

A Companion Package for the Book "A Course in Statistics with R"

ACTCD

Asymptotic Classification Theory for Cognitive Diagnosis

Actigraphy

Actigraphy Data Analysis

activity

Animal Activity Statistics

activpalProcessing

Process activPAL Events Files

actuar

Actuarial Functions and Heavy Tailed Distributions

ActuDistns

Functions for actuarial scientists

ada

The R Package Ada for Stochastic Boosting

adabag

Applies Multiclass AdaBoost.M1, SAMME and Bagging

ADaCGH2

Analysis of big data from aCGH experiments using parallel computing and ff objects

adagio

Discrete and Global Optimization Routines

adagio

Discrete and Global Optimization Routines

AdapEnetClass

A Class of Adaptive Elastic Net Methods for Censored Data

adapr

Implementation of an Accountable Data Analysis Process

adaptDA

Adaptive Mixture Discriminant Analysis

AdaptFit

Adaptive Semiparametic Regression

AdaptFitOS

Adaptive Semiparametric Regression with Simultaneous Confidence Bands

AdaptGauss

Gaussian Mixture Models (GMM)

AdaptiveSparsity

Adaptive Sparsity Models

adaptivetau

Tau-Leaping Stochastic Simulation

adaptMCMC

Implementation of a generic adaptive Monte Carlo Markov Chain sampler

adaptsmoFMRI

Adaptive Smoothing of FMRI Data

adaptTest

Adaptive two-stage tests

ADCT

Adaptive Design in Clinical Trials

addhaz

Binomial and Multinomial Additive Hazards Models

addhazard

Fit Additive Hazards Models for Survival Analysis

addinslist

Discover and Install Useful RStudio Addins

additivityTests

Additivity Tests in the Two Way Anova with Single Sub-class Numbers

addreg

Additive Regression for Discrete Data

ADDT

Analysis of Accelerated Destructive Degradation Test Data

ade4

Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

ade4

Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

ade4TkGUI

'ade4' Tcl/Tk Graphical User Interface

ade4TkGUI

'ade4' Tcl/Tk Graphical User Interface

adegenet

Exploratory Analysis of Genetic and Genomic Data

adegraphics

An S4 Lattice-Based Package for the Representation of Multivariate Data

adegraphics

An S4 Lattice-Based Package for the Representation of Multivariate Data

adehabitat

Analysis of Habitat Selection by Animals

adehabitatHR

Home Range Estimation

adehabitatHS

Analysis of Habitat Selection by Animals

adehabitatLT

Analysis of Animal Movements

adehabitatMA

Tools to Deal with Raster Maps

adephylo

adephylo: exploratory analyses for the phylogenetic comparative method.

adephylo

Adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

AdequacyModel

Adequacy of Probabilistic Models and General Purpose Optimization

adespatial

Multivariate Multiscale Spatial Analysis

adespatial

Multivariate Multiscale Spatial Analysis

ADGofTest

Anderson-Darling GoF test

ADGofTest

Anderson-Darling GoF test

adhoc

calculate ad hoc distance thresholds for DNA barcoding identification

adimpro

Adaptive Smoothing of Digital Images

AdjBQR

Adjusted Bayesian Quantile Regression Inference

adlift

An adaptive lifting scheme algorithm

ADM3

An Interpretation of the ADM method - automated detection algorithm.

admbsecr

SECR models with supplementary location information

AdMit

Adaptive Mixture of Student-t Distributions

admixturegraph

Admixture Graph Manipulation and Fitting

ADMMnet

Regularized Model with Selecting the Number of Non-Zeros

ADPclust

Fast Clustering Using Adaptive Density Peak Detection

ads

Spatial point patterns analysis

adSplit

Annotation-Driven Clustering

AdvBinomApps

Upper Clopper-Pearson Confidence Limits for Burn-in Studies under Additional Available Information

advclust

Object Oriented Advanced Clustering

advclust

Object Oriented Advanced Clustering

advfclust

Fuzzy Clustering (Ensembling and Optimization)

adwave

Wavelet Analysis of Genomic Data from Admixed Populations

AEDForecasting

Change Point Analysis in ARIMA Forecasting

AEM

Tools to construct Asymmetric eigenvector maps (AEM) spatial variables

aemo

Download and Process AEMO Price and Demand Data

AER

Applied Econometrics with R

AF

Model-Based Estimation of Confounder-Adjusted Attributable Fractions

afe

Analysis of Factorial Experiments

afex

Analysis of Factorial Experiments

afex

Analysis of Factorial Experiments

affxparser

Affymetrix File Parsing SDK

affy

Methods for Affymetrix Oligonucleotide Arrays

affycomp

Graphics Toolbox for Assessment of Affymetrix Expression Measures

AffyCompatible

Affymetrix GeneChip software compatibility

affyContam

structured corruption of affymetrix cel file data

affycoretools

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

AffyExpress

Affymetrix Quality Assessment and Analysis Tool

affyILM

Linear Model of background subtraction and the Langmuir isotherm

affyio

Tools for parsing Affymetrix data files

affylmGUI

GUI for limma package with Affymetrix microarrays

affyPara

Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

affypdnn

Probe Dependent Nearest Neighbours (PDNN) for the affy package

affyPLM

Methods for fitting probe-level models

affyQCReport

QC Report Generation for affyBatch objects

AffyRNADegradation

Analyze and correct probe positional bias in microarray data due to RNA degradation

AffyTiling

Easy extraction of individual probes in Affymetrix tiling arrays

AFLP

Analysis of AFLP data

AFLPsim

Hybrid Simulation and Genome Scan for Dominant Markers

AFM

Atomic Force Microscope Image Analysis

after

Run Code in the Background

aftgee

Accelerated Failure Time Model with Generalized Estimating Equations

AGD

Analysis of Growth Data

AGDEX

Agreement of Differential Expression Analysis

AggregateR

Aggregate Numeric, Date and Categorical Variables by an ID

agilp

Agilent expression array processing package

AgiMicroRna

Processing and Differential Expression Analysis of Agilent microRNA chips

agop

Aggregation Operators and Preordered Sets

agRee

Various Methods for Measuring Agreement

Agreement

Statistical Tools for Measuring Agreement

agricolae

Statistical Procedures for Agricultural Research

agridat

Agricultural Datasets

agrmt

Calculate Agreement or Consensus in Ordered Rating Scales

agrmt

Calculate Agreement or Consensus in Ordered Rating Scales

AGSDest

Estimation in Adaptive Group Sequential Trials

agsemisc

Miscellaneous plotting and utility functions

ahaz

Regularization for semiparametric additive hazards regression

AhoCorasickTrie

Fast Searching for Multiple Keywords in Multiple Texts

ahp

Analytic Hierarchy Process

AHR

Estimation and Testing of Average Hazard Ratios

AICcmodavg

Model Selection and Multimodel Inference Based on (Q)AIC(c)

AID

Estimation of Box-Cox Power Transformation Parameter

aidar

Tools for reading AIDA (http://aida.freehep.org/) files into R

AIG

Automatic Item Generator

AIM

AIM: adaptive index model

aimPlot

Create Pie Like Plot for Completeness

AIMS

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

Ake

Associated Kernel Estimations

akima

Interpolation of Irregularly and Regularly Spaced Data

akmeans

Adaptive Kmeans algorithm based on threshold

ALA

Data sets and examples for the book "Applied Longitudinal Analysis"

ALA4R

Atlas of Living Australia (ALA) Data and Resources in R

alabama

Constrained nonlinear optimization

alabama

Constrained Nonlinear Optimization

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

ald

The Asymmetric Laplace Distribution

ALDEx2

Analysis Of Differential Abundance Taking Sample Variation Into Account

ALDqr

Quantile Regression Using Asymmetric Laplace Distribution

alfa

Apache Log File Analysis

aLFQ

Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

AlgDesign

Algorithmic Experimental Design

AlgebraicHaploPackage

Haplotype Two Snips Out of a Paired Group of Patients

algorithmia

Allows you to Easily Interact with the Algorithmia Platform

algstat

Algebraic statistics in R

AlignStat

Comparison of Alternative Multiple Sequence Alignments

alineR

Alignment of Phonetic Sequences Using the 'ALINE' Algorithm

ALKr

Generate Age-Length Keys for fish populations

allan

Automated Large Linear Analysis Node

allanvar

Allan Variance Analysis

alleHap

Allele Imputation and Haplotype Reconstruction from Pedigree Databases

allelematch

Identifying unique multilocus genotypes where genotyping error and missing data may be present

AlleleRetain

Allele Retention, Inbreeding, and Demography

allelic

A fast, unbiased and exact allelic exact test

AllelicImbalance

Investigates Allele Specific Expression

AllPossibleSpellings

Computes all of a word's possible spellings.

alluvial

Alluvial Diagrams

alm

R Client for the Lagotto Altmetrics Platform

alpha

Robust Cronbach's alpha with missing and non-normal data

alphahull

Generalization of the Convex Hull of a Sample of Points in the Plane

alphaOutlier

Obtain Alpha-Outlier Regions for Well-Known Probability Distributions

alphashape3d

Implementation of the 3D Alpha-Shape for the Reconstruction of 3D Sets from a Point Cloud

alpine

alpine

alplot

Plot array lists

alr

alternating logistic regression

alr3

Data to accompany Applied Linear Regression 3rd edition

alr3

Data to accompany Applied Linear Regression 3rd edition

alr4

Data to accompany Applied Linear Regression 4th edition

alr4

Data to accompany Applied Linear Regression 4rd edition

ALS

Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)

alsace

ALS for the Automatic Chemical Exploration of mixtures

ALSCPC

Accelerated line search algorithm for simultaneous orthogonal transformation of several positive definite symmetric matrices to nearly diagonal form.

ALSM

Companion to Applied Linear Statistical Models

altcdfenvs

alternative CDF environments (aka probeset mappings)

altmeta

Alternative Meta-Analysis Methods

ALTopt

Optimal Experimental Designs for Accelerated Life Testing

amap

Another Multidimensional Analysis Package

AMAP.Seq

Compare Gene Expressions from 2-Treatment RNA-Seq Experiments

ambur

Analyzing Moving Boundaries Using R

amburhva

AMBUR-HVA

AMCP

A Multiple Comparison Perspective

ameco

European Commission Annual Macro-Economic (AMECO) Database

amei

Adaptive Management of Epidemiological Interventions

Amelia

A Program for Missing Data

amen

Additive and Multiplicative Effects Models for Networks and Relational Data

AmericanCallOpt

This package includes pricing function for selected American call options with underlying assets that generate payouts.

AMGET

Post-processing tool for ADAPT 5

aml

Adaptive Mixed LASSO

AMModels

Adaptive Management Model Manager

AmmoniaConcentration

Un-Ionized Ammonia Concentration

AMOEBA

A Multidirectional Optimum Ecotope-Based Algorithm

AMORE

A MORE flexible neural network package

AmostraBrasil

Generates Samples or Complete List of Brazilian IBGE (Instituto Brasileiro De Geografia e Estatistica) Census Households, Geocoding it by Google Maps

AMOUNTAIN

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

ampd

An Algorithm for Automatic Peak Detection in Noisy Periodic and Quasi-Periodic Signals

AmpliconDuo

Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

ampliQueso

Analysis of amplicon enrichment panels

AmyloGram

Prediction of Amyloid Proteins

anacor

Simple and Canonical Correspondence Analysis

analogsea

Interface to 'Digital Ocean'

analogue

Analogue and Weighted Averaging Methods for Palaeoecology

analogueExtra

Additional Functions for Use with the Analogue Package

AnalysisPageServer

A framework for sharing interactive data and plots from R through the web.

analyz

Model Layer for Automatic Data Analysis via CSV File Interpretation

AnalyzeFMRI

Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format.

AnalyzeTS

Analyze Fuzzy Time Series

anametrix

Bidirectional Connector to Anametrix API

anamiR

An integrated analysis package of miRNA and mRNA expression data

anapuce

Tools for microarray data analysis

Anaquin

Statistical analysis of sequins

AncestryMapper

Assigning Ancestry Based on Population References

anchors

Statistical analysis of surveys with anchoring vignettes

AnDE

An extended Bayesian Learning Technique developed by Dr. Geoff Webb

andrews

Andrews curves

anesrake

ANES Raking Implementation

AneuFinder

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

anfis

Adaptive Neuro Fuzzy Inference System in R

AnglerCreelSurveySimulation

Simulate a Bus Route Creel Survey of Anglers

Animal

Analyze time-coded animal behavior data

animalTrack

Animal track reconstruction for high frequency 2-dimensional (2D) or 3-dimensional (3D) movement data.

animation

A Gallery of Animations in Statistics and Utilities to Create Animations

anim.plots

Simple Animated Plots For R

ANLP

Build Text Prediction Model

ANN

Feedforward Artificial Neural Network optimized by Genetic Algorithm

annaffy

Annotation tools for Affymetrix biological metadata

annmap

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

annotate

Annotation for microarrays

AnnotationDbi

Annotation Database Interface

AnnotationForge

Code for Building Annotation Database Packages

AnnotationFuncs

Annotation translation functions

AnnotationHub

Client to access AnnotationHub resources

AnnotationHubData

Transform public data resources into Bioconductor Data Structures

annotationTools

Annotate microarrays and perform cross-species gene expression analyses using flat file databases.

annotatr

Annotation of Genomic Regions to Genomic Annotations

AnnotLists

AnnotLists: A tool to annotate multiple lists from a specific annotation file.

anocva

A Non-Parametric Statistical Test to Compare Clustering Structures

anoint

Analysis of Interactions

ANOM

Analysis of Means

anominate

alpha-NOMINATE Ideal Point Estimator

anonymizer

Anonymize Data Containing Personally Identifiable Information

anota

ANalysis Of Translational Activity (ANOTA).

ant

Version of ant specific to R

AntAngioCOOL

Anti-Angiogenic Peptide Prediction

AnthropMMD

A GUI for Mean Measures of Divergence

Anthropometry

Statistical Methods for Anthropometric Data

antiProfiles

Implementation of gene expression anti-profiles

antitrust

Tools for Antitrust Practitioners

AntWeb

programmatic interface to the AntWeb

anytime

Anything to 'POSIXct' or 'Date' Converter

aod

Analysis of Overdispersed Data

aods3

Analysis of Overdispersed Data using S3 methods

aoos

Another Object Orientation System

aop

Adverse Outcome Pathway Analysis

aoristic

aoristic analysis with spatial output (kml)

apa

Format Outputs of Statistical Tests According to APA Guidelines

ApacheLogProcessor

Process the Apache Web Server Access Log Files

apaStyle

Generate APA Tables for MS Word

apaTables

Create American Psychological Association (APA) Style Tables

apc

Age-Period-Cohort Analysis

apcluster

Affinity Propagation Clustering

apComplex

Estimate protein complex membership using AP-MS protein data

apdesign

An Implementation of the Additive Polynomial Design Matrix

ape

Analyses of Phylogenetics and Evolution

apex

Phylogenetic Methods for Multiple Gene Data

APfun

Geo-Processing Base Functions

apicultuR

A wrapper to the apicultuR set of APIs for NLP in Spanish

aplore3

Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic Regression" (3rd Ed., 2013)

aplpack

Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, plotsummary, plothulls, and some slider functions

apmsWAPP

Pre- and Postprocessing for AP-MS data analysis based on spectral counts

appell

Compute Appell's F1 hypergeometric function

apple

Approximate Path for Penalized Likelihood Estimators

AppliedPredictiveModeling

Functions and Data Sets for 'Applied Predictive Modeling'

AppliedPredictiveModeling

Functions and Data Sets for 'Applied Predictive Modeling'

appnn

Amyloid Propensity Prediction Neural Network

approximator

Bayesian prediction of complex computer codes

APR

Applied Psychometrics With R

aprean3

Datasets from Draper and Smith "Applied Regression Analysis" (3rd Ed., 1998)

apricom

Tools for the a Priori Comparison of Regression Modelling Strategies

aprof

Amdahl's Profiler, Directed Optimization Made Easy

APSIM

General Utility Functions for the 'Agricultural Production Systems Simulator'

APSIMBatch

Analysis the output of Apsim software

apsimr

Edit, Run and Evaluate APSIM Simulations Easily Using R

apsrtable

apsrtable model-output formatter for social science

apt

Asymmetric Price Transmission

APtools

Average Positive Predictive Values (AP) for Binary Outcomes and Censored Event Times

apTreeshape

Analyses of Phylogenetic Treeshape

aqfig

Functions to help display air quality model output and monitoring data

aqp

Algorithms for Quantitative Pedology

aqp

Algorithms for Quantitative Pedology

aqr

Interface methods to use with an ActiveQuant Master Server

aqr

Interface methods to use with an ActiveQuant Master Server

AquaEnv

Integrated Development Toolbox for Aquatic Chemical Model Generation

AquaEnv

Integrated Development Toolbox for Aquatic Chemical Model Generation

AR1seg

Segmentation of an autoregressive Gaussian process of order 1

arabicStemR

Arabic Stemmer for Text Analysis

ArArRedux

Rigorous Data Reduction and Error Propagation of Ar40 / Ar39 Data

arc

Association Rule Classification

ARCensReg

Fitting Univariate Censored Linear Regression Model with Autoregressive Errors

archdata

Example Datasets from Archaeological Research

archetypes

Archetypal Analysis

archetypes

Archetypal Analysis

archiDART

Plant Root System Architecture Analysis Using DART and RSML Files

archivist

Tools for Storing, Restoring and Searching for R Objects

archivist.github

Tools for Archiving, Managing and Sharing R Objects via GitHub

ArDec

Time series autoregressive-based decomposition

arf3DS4

Activated Region Fitting, fMRI data analysis (3D).

arf3DS4

Activated Region Fitting, fMRI data analysis (3D).

arfima

Fractional ARIMA (and Other Long Memory) Time Series Modeling

ArfimaMLM

Arfima-MLM Estimation For Repeated Cross-Sectional Data

arfS4

Activated Region Fitting, fMRI data analysis.

argosfilter

Argos locations filter

argparse

Command Line Optional and Positional Argument Parser

argparser

Command-Line Argument Parser

ArgumentCheck

Improved Communication to Users with Respect to Problems in Function Arguments

arm

Data Analysis Using Regression and Multilevel/Hierarchical Models

arm

Data Analysis Using Regression and Multilevel/Hierarchical Models

arnie

"Arnie" box office records 1982-2014

aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

aroma.apd

A probe-level data file format used by aroma.affymetrix [DEPRECATED]

aroma.apd

A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]

aroma.cn

Copy-Number Analysis of Large Microarray Data Sets

aroma.core

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

aroma.light

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

aroma.tcga

Methods for accessing online The Cancer Genome Atlas (TCGA) data

ARPobservation

Tools for Simulating Direct Behavioral Observation Recording Procedures Based on Alternating Renewal Processes

aRpsDCA

Arps Decline Curve Analysis in R

arrApply

Apply a Function to a Margin of an Array

array

Array factor for 2D periodic arrays

ArrayBin

Binarization of numeric data arrays

ArrayExpress

Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

ArrayExpressHTS

ArrayExpress High Throughput Sequencing Processing Pipeline

arrayhelpers

Convenience Functions for Arrays

arrayhelpers

Convenience Functions for Arrays

arrayMvout

multivariate outlier detection for expression array QA

arrayQuality

Assessing array quality on spotted arrays

arrayQualityMetrics

Quality metrics report for microarray data sets

ArrayTools

geneChip Analysis Package

ArrayTV

Implementation of wave correction for arrays

ARRmNormalization

Adaptive Robust Regression normalization for Illumina methylation data

ars

Adaptive Rejection Sampling

arsenal

An Arsenal of 'R' Functions for Large-Scale Statistical Summaries

ART

Aligned Rank Transform for Nonparametric Factorial Analysis

artfima

ARTFIMA Model Estimation

ARTIVA

Time-Varying DBN Inference with the ARTIVA (Auto Regressive TIme VArying) Model

ARTool

Aligned Rank Transform

ARTP

Gene and Pathway p-values computed using the Adaptive Rank Truncated Product

ARTP2

Pathway and Gene-Level Association Test

arules

Mining Association Rules and Frequent Itemsets

arulesCBA

Classification Based on Association Rules

arulesNBMiner

Mining NB-Frequent Itemsets and NB-Precise Rules

arulesNBMiner

Mining NB-Frequent Itemsets and NB-Precise Rules

arulesSequences

Mining Frequent Sequences

arulesViz

Visualizing Association Rules and Frequent Itemsets

arulesViz

Visualizing Association Rules and Frequent Itemsets

arulesVizOld

arulesViz - Visualizing Association Rules and Frequent Itemsets

aRxiv

Interface to the arXiv API

ASAFE

Ancestry Specific Allele Frequency Estimation

ASAtable

Model-output formatter for sociological research.

asaur

Data Sets for "Applied Survival Analysis Using R""

asbio

A Collection of Statistical Tools for Biologists

ascii

Export R objects to several markup languages

as.color

Assign Random Colors to Unique Items in a Vector

asd

Simulations for Adaptive Seamless Designs

asdreader

Reading ASD Binary Files in R

ASEB

Predict Acetylated Lysine Sites

ASGSCA

Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models

ash

David Scott's ASH Routines

ashr

Methods for Adaptive Shrinkage, using Empirical Bayes

asht

Applied Statistical Hypothesis Tests

AsioHeaders

'Asio' C++ Header Files

aslib

Interface to the Algorithm Selection Benchmark Library

ASMap

Linkage Map Construction using the MSTmap Algorithm

asmn

All sample mean normalization.

asnipe

Animal Social Network Inference and Permutations for Ecologists

aspace

A collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns

ASPBay

Bayesian Inference on Causal Genetic Variants using Affected Sib-Pairs Data

aspect

A General Framework for Multivariate Analysis with Optimal Scaling

aspect

A General Framework for Multivariate Analysis with Optimal Scaling

aspi

Analysis of Symmetry of Parasitic Infections

ASpli

Analysis of alternative splicing using RNA-Seq

aSPU

Adaptive Sum of Powered Score Test

asremlPlus

Augments the Use of 'ASReml-R' in Fitting Mixed Models

AssayCorrector

Detection and Correction of Spatial Bias in HTS Screens

assertable

Verbose Assertions for Tabular Data (Data.frames and Data.tables)

assertive

Readable Check Functions to Ensure Code Integrity

assertive.base

A Lightweight Core of the 'assertive' Package

assertive.code

Assertions to Check Properties of Code

assertive.data

Assertions to Check Properties of Data

assertive.data.uk

Assertions to Check Properties of Strings

assertive.data.us

Assertions to Check Properties of Strings

assertive.datetimes

Assertions to Check Properties of Dates and Times

assertive.files

Assertions to Check Properties of Files

assertive.matrices

Assertions to Check Properties of Matrices

assertive.models

Assertions to Check Properties of Models

assertive.numbers

Assertions to Check Properties of Numbers

assertive.properties

Assertions to Check Properties of Variables

assertive.reflection

Assertions for Checking the State of R

assertive.sets

Assertions to Check Properties of Sets

assertive.strings

Assertions to Check Properties of Strings

assertive.types

Assertions to Check Types of Variables

assertr

Assertive Programming for R Analysis Pipelines

assertthat

Easy pre and post assertions.

ASSET

An R package for subset-based association analysis of heterogeneous traits and subtypes

ASSET

An R package for subset-based association analysis of heterogeneous traits and subtypes

AssetPricing

Optimal pricing of assets with fixed expiry date.

ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

assignPOP

Population Assignment using Genomic, Non-Genetic or Integrated Data in a Machine-Learning Framework

assist

A Suite of R Functions Implementing Spline Smoothing Techniques

ASSISTant

Adaptive Subgroup Selection in Group Sequential Trials

AssocTests

Genetic Association Studies

assortnet

Calculate the Assortativity Coefficient of Weighted and Binary Networks

AssotesteR

Statistical Tests for Genetic Association Studies

aster

Aster Models

aster2

Aster Models

astro

Astronomy Functions, Tools and Routines

astrochron

A Computational Tool for Astrochronology

astrodatR

Astronomical Data

astroFns

Astronomy: time and position functions, misc. utilities

astrolibR

Astronomy Users Library

astsa

Applied Statistical Time Series Analysis

asuR

Advanced statistics using R

asVPC

Average Shifted Visual Predictive Checks

asymLD

Asymmetric Linkage Disequilibrium (ALD) for Polymorphic Genetic Data

asymmetry

Visualizing Asymmetric Data

asympTest

Asymptotic statistic

AsynchLong

Regression Analysis of Sparse Asynchronous Longitudinal Data

asypow

Calculate Power Utilizing Asymptotic Likelihood Ratio Methods

ATE

Inference for Average Treatment Effects using Covariate Balancing

AtelieR

A GTK GUI for teaching basic concepts in statistical inference, and doing elementary bayesian tests.

AtelieR

A GTK GUI for teaching basic concepts in statistical inference, and doing elementary bayesian tests.

AtlasRDF

Gene Expression Atlas query and gene set enrichment package.

atmcmc

Automatically Tuned Markov Chain Monte Carlo

ATmet

Advanced Tools for Metrology

atmosphere

weather and climate analysis

AtmRay

Acoustic Traveltime Calculations for 1-D Atmospheric Models

Atools

Atools

aTSA

Alternative Time Series Analysis

atsd

Support Querying Axibase Time-Series Database

attract

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

attrCUSUM

Tools for Attribute VSI CUSUM Control Chart

attribrisk

Population Attributable Risk

AUC

Threshold independent performance measures for probabilistic classifiers.

aucm

AUC Maximization

AUCRF

Variable Selection with Random Forest and the Area Under the Curve

audio

Audio Interface for R

audiolyzR

audiolyzR: Give your data a listen

audit

Bounds for Accounting Populations

audited

Automatic Tracing and Display of Changes to Row Count

aurelhy

Hydrometeorological interpolation

auRoc

Various Methods to Estimate the AUC

austin

A package for doing things with words

AUtests

Approximate Unconditional and Permutation Tests

autocorr

Testing Autocorrelation through bootstrap and surrogate methods

AutoDeskR

An Interface to the 'AutoDesk' 'API'

autoencoder

Sparse Autoencoder for Automatic Learning of Representative Features from Unlabeled Data

autoimage

Display Multiple Images with Scaled Colors

automap

Automatic interpolation package

AutoModel

Automated Hierarchical Multiple Regression with Assumptions Checking

automultinomial

Autologistic and Automultinomial Spatial Regression and Variable Selection

autopls

Partial Least Squares Regression with Backward Selection of Predictors

AutoregressionMDE

Minimum Distance Estimation in Autoregressive Model

AutoSEARCH

General-to-Specific (GETS) Modelling

autoSEM

Performs Specification Search in Structural Equation Models

autovarCore

Automated Vector Autoregression Models and Networks

averisk

Calculation of Average Population Attributable Fractions and Confidence Intervals

aVirtualTwins

Adaptation of Virtual Twins Method from Jared Foster

aws

Adaptive Weights Smoothing

aws.alexa

Client for the Amazon Alexa Web Information Services API

aws.ec2metadata

Get EC2 Instance Metadata

awsjavasdk

Boilerplate R Access to the Amazon Web Services ('AWS') Java SDK

awsMethods

Class and Methods Definitions for Packages 'aws', 'adimpro', 'fmri', 'dwi'

aws.polly

Client for AWS Polly

aws.ses

AWS SES Client Package

aws.signature

Amazon Web Services Request Signatures

aws.sns

AWS SNS Client Package

aws.sqs

AWS SQS Client Package

aylmer

A generalization of Fisher's exact test

AzureML

Interface with Azure Machine Learning Datasets, Experiments and Web Services

B2Z

Bayesian Two-Zone Model

b6e6rl

Adaptive differential evolution, b6e6rl variant

BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

babar

Bayesian Bacterial Growth Curve Analysis in R

babel

Ribosome Profiling Data Analysis

BaBooN

Bayesian Bootstrap Predictive Mean Matching - Multiple and Single Imputation for Discrete Data

babynames

US Baby Names 1880-2014

BAC

Bayesian Analysis of Chip-chip experiment

BACA

Bubble Chart to Compare Biological Annotations by using DAVID

BacArena

Modeling Framework for Cellular Communities in their Environments

BACCO

Bayesian Analysis of Computer Code Output (BACCO)

BACCT

Bayesian Augmented Control for Clinical Trials

backblazer

Bindings to the Backblaze B2 API

background

This packages allow users to ``background'' computations.

backpipe

Backward Pipe Operator

backports

Reimplementations of Functions Introduced Since R-3.0.0

backShift

Learning Causal Cyclic Graphs from Unknown Shift Interventions

backtest

Exploring Portfolio-Based Conjectures About Financial Instruments

backtestGraphics

Interactive Graphics for Portfolio Data

bacon

Controlling bias and inflation in association studies using the empirical null distribution

BACprior

Choice of the Hyperparameter Omega in the Bayesian Adjustment for Confounding (BAC) Algorithm

bacr

Bayesian Adjustment for Confounding

BADER

Bayesian Analysis of Differential Expression in RNA Sequencing Data

badgecreatr

Create Badges for 'Travis', 'Repostatus' 'Codecov.io' Etc in Github Readme

BADGER

A package for identifying sample mixups in combined expression and genotyping studies.

BadRegionFinder

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

BAEssd

Bayesian Average Error approach to Sample Size Determination

Bagidis

BAses GIving DIStances

bagRboostR

Ensemble bagging and boosting classifiers

BAGS

A Bayesian Approach for Geneset Selection

baitmet

Library Driven Compound Profiling in GC-MS Data

BalanceCheck

Balance Check for Multiple Covariates in Matched Observational Studies

BalancedSampling

Balanced and Spatially Balanced Sampling

ballgown

Flexible, isoform-level differential expression analysis

BaM

Functions and Datasets for Books by Jeff Gill

BAMBI

Bivariate Angular Mixture Models

bamdit

Bayesian Meta-Analysis of Diagnostic Test Data

bamlss

Bayesian Additive Models for Location Scale and Shape (and Beyond)

BAMMtools

Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

bamsignals

Extract read count signals from bam files

bandit

Functions for simple A/B split test and multi-armed bandit analysis

BANFF

Bayesian Network Feature Finder

bannerCommenter

Make Banner Comments with a Consistent Format

BANOVA

Hierarchical Bayesian ANOVA Models

banxicoR

Download Data from the Bank of Mexico

BAPC

Projection of cancer incidence and mortality data using Bayesian APC models fitted with INLA

bapred

Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)

BaPreStoPro

Bayesian Prediction of Stochastic Processes

barcode

Barcode distribution plots

barcode

Barcode distribution plots

BarcodingR

Species Identification using DNA Barcodes

barebone

Multivariate Methods in Ecology with R: Basic Algorithms

Barnard

Barnard's Unconditional Test

bartMachine

Bayesian Additive Regression Trees

bartMachineJARs

bartMachine JARs

Barycenter

Wasserstein Barycenter

BAS

Bayesian Model Averaging using Bayesian Adaptive Sampling

base64

Base 64 encoder/decoder

base64

Base64 Encoder and Decoder

base64enc

Tools for base64 encoding

base64url

Fast and URL-Safe Base64 Encoder and Decoder

basefun

Infrastructure for Computing with Basis Functions

basefun

Infrastructure for Computing with Basis Functions

baseline

Baseline Correction of Spectra

BaseSpaceR

R SDK for BaseSpace RESTful API

Basic4Cseq

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

basicspace

Recovering a Basic Space from Issue Scales

BasicSTARRseq

Basic peak calling on STARR-seq data

BASIX

BASIX: An efficient C/C++ toolset for R.

BASS

Bayesian Adaptive Spline Surfaces

BaSTA

Age-Specific Survival Analysis from Incomplete Capture-Recapture/Recovery Data

bastah

Big Data Statistical Analysis for High-Dimensional Models

BAT

Biodiversity Assessment Tools

batade

HTML reports and so on

batch

Batching Routines in Parallel and Passing Command-Line Arguments to R

BatchExperiments

Statistical Experiments on Batch Computing Clusters

BatchGetSymbols

Downloads and Organizes Financial Data for Multiple Tickers

BatchJobs

Batch Computing with R

batchmeans

Consistent Batch Means Estimation of Monte Carlo Standard Errors

BatchQC

Batch Effects Quality Control Software

batchtools

Tools for Computation on Batch Systems

batman

Convert Categorical Representations of Logicals to Actual Logicals

batman

Bayesian AuTomated Metabolite Analyser for NMR spectra

batteryreduction

An R Package for Data Reduction by Battery Reduction

baybi

Bayesian Biclustering with Subject and Variable Importance

BayClone2

Bayesian Feature Allocation Model for Tumor Heterogeneity

bayesAB

Fast Bayesian Methods for AB Testing

BayesBD

Bayesian Inference for Image Boundaries

BayesBinMix

Bayesian Estimation of Mixtures of Multivariate Bernoulli Distributions

bayesbio

Miscellaneous Functions for Bioinformatics and Bayesian Statistics

bayesboot

An Implementation of Rubin's (1981) Bayesian Bootstrap

BayesBridge

Bridge Regression

BayesComm

Bayesian Community Ecology Analysis

bayescount

Power Calculations and Bayesian Analysis of Count Distributions and FECRT Data using MCMC

BayesCR

Bayesian Analysis of Censored Regression Models Under Scale Mixture of Skew Normal Distributions

BayesDA

Functions and Datasets for the book "Bayesian Data Analysis"

bayesDccGarch

The Bayesian Dynamic Conditional Correlation GARCH Model

bayesDem

Graphical User Interface for bayesTFR, bayesLife and bayesPop

bayesdnamix

Procedure for evaluate marginal likelihood for quantitative STR DNA mixture bayesian models

BayesFactor

Computation of Bayes Factors for Common Designs

BayesFactor

Computation of Bayes factors for common designs

BayesFactors.gibi

Compute Bayes factors using the GIBI interface

BayesFM

Bayesian Inference for Factor Modeling

bayesGARCH

Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations

bayesGDS

Scalable Rejection Sampling for Bayesian Hierarchical Models

BayesGESM

Bayesian Analysis of Generalized Elliptical Semi-Parametric Models and Flexible Measurement Error Models

BayesH

Bayesian Regression Model with Mixture of Two Scaled Inverse Chi Square as Hyperprior

BayesianAnimalTracker

Bayesian Melding of GPS and DR Path for Animal Tracking

Bayesianbetareg

Bayesian Beta regression: joint mean and precision modeling

bayesianETAS

Bayesian Estimation of the ETAS Model for Earthquake Occurrences

BayesianNetwork

Bayesian Network Modeling and Analysis

bayesImageS

Bayesian Methods for Image Segmentation using a Potts Model

BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

BayesLCA

Bayesian Latent Class Analysis

bayesLife

Bayesian Projection of Life Expectancy

BayesLogit

Logistic Regression

bayesloglin

Bayesian Analysis of Contingency Table Data

bayesm

Bayesian Inference for Marketing/Micro-Econometrics

BayesMAMS

Designing Bayesian Multi-Arm Multi-Stage Studies

bayesMCClust

Mixtures-of-Experts Markov Chain Clustering and Dirichlet Multinomial Clustering

BayesMed

Default Bayesian Hypothesis Tests for Correlation, Partial Correlation, and Mediation

bayesmeta

Bayesian Random-Effects Meta-Analysis

bayesmix

Bayesian Mixture Models with JAGS

BayesMixSurv

Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification

BayesNI

BayesNI: Bayesian Testing Procedure for Noninferiority with Binary Endpoints

BayesPeak

Bayesian Analysis of ChIP-seq Data

BayesPiecewiseICAR

Hierarchical Bayesian Model for a Hazard Function

bayesplot

Plotting for Bayesian Models

bayesPop

Probabilistic Population Projection

bayespref

Hierarchical Bayesian analysis of ecological count data

bayesQR

Bayesian quantile regression

BayesR

Bayesian Regression in R

bayesreg

Bayesian Regression Models with Continuous Shrinkage Priors

bayess

Bayesian Essentials with R

BayesS5

Bayesian Variable Selection Using Simplified Shotgun Stochastic Search with Screening (S5)

BayesSAE

Bayesian Analysis of Small Area Estimation

BayesSingleSub

Computation of Bayes factors for interrupted time-series designs

BayesSingleSub

Computation of Bayes factors for interrupted time-series designs

BayesSummaryStatLM

MCMC Sampling of Bayesian Linear Models via Summary Statistics

bayesSurv

Bayesian Survival Regression with Flexible Error and Random Effects Distributions

bayesTFR

Bayesian Fertility Projection

Bayesthresh

Bayesian thresholds mixed-effects models for categorical data

BayesTree

Bayesian Additive Regression Trees

BayesTreePrior

Bayesian Tree Prior Simulation

BayesValidate

BayesValidate Package

BayesVarSel

Bayes Factors, Model Choice and Variable Selection in Linear Models

BayesX

R Utilities Accompanying the Software Package BayesX

BayesXdev

R Package Distribution of the BayesX C++ Development Sources

BayesXsrc

R Package Distribution of the BayesX C++ Sources

BayHap

Bayesian analysis of haplotype association using Markov Chain Monte Carlo

BayHaz

R Functions for Bayesian Hazard Rate Estimation

BaylorEdPsych

R Package for Baylor University Educational Psychology Quantitative Courses

bayou

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

baySeq

Empirical Bayesian analysis of patterns of differential expression in count data

BaySIC

Bayesian Analysis of Significantly Mutated Genes in Cancer

BAYSTAR

On Bayesian analysis of Threshold autoregressive model (BAYSTAR)

bazar

Miscellaneous Basic Functions

BB

Solving and Optimizing Large-Scale Nonlinear Systems

BB

Solving and Optimizing Large-Scale Nonlinear Systems

BBCAnalyzer

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

bbefkr

Bayesian bandwidth estimation and semi-metric selection for the functional kernel regression with unknown error density

bbemkr

Bayesian bandwidth estimation for multivariate kernel regression with Gaussian error

BBEST

Bayesian Estimation of Incoherent Neutron Scattering Backgrounds

BBmisc

Miscellaneous Helper Functions for B. Bischl

bbmle

Tools for General Maximum Likelihood Estimation

bbmle

Tools for general maximum likelihood estimation

BBMM

Brownian bridge movement model

bbo

Biogeography-Based Optimization

BBRecapture

Bayesian Behavioural Capture-Recapture Models

bc3net

Gene Regulatory Network Inference with Bc3net

BCA

Business and Customer Analytics

BCBCSF

Bias-Corrected Bayesian Classification with Selected Features

BCDating

Business Cycle Dating and Plotting Tools

BcDiag

Diagnostics Plots for Bicluster Data

BcDiag

Diagnostics Plots for Bicluster Data

BCE

Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data

BCE

Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data

BCEA

Bayesian Cost Effectiveness Analysis

BCEE

The Bayesian Causal Effect Estimation Algorithm

BCellMA

B Cell Receptor Somatic Hyper Mutation Analysis

BCEs0

Bayesian Models for Cost-Effectiveness Analysis in the Presence of Structural Zero Costs

Bchron

Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling

Bclim

Bayesian Palaeoclimate Reconstruction from Pollen Data

bclust

Bayesian Hierarchical Clustering Using Spike and Slab Models

bclust

Bayesian Hierarchical Clustering Using Spike and Slab Models

bcp

Bayesian Analysis of Change Point Problems

bcpa

Behavioral change point analysis of animal movement

bcpmeta

Bayesian Multiple Changepoint Detection Using Metadata

BCRA

Breast Cancer Risk Assessment

BCRANK

Predicting binding site consensus from ranked DNA sequences

bcRep

Advanced Analysis of B Cell Receptor Repertoire Data

bcrm

Bayesian Continual Reassessment Method for Phase I Dose-Escalation Trials

bcROCsurface

Bias-Corrected Methods for Estimating the ROC Surface of Continuous Diagnostic Tests

bcrypt

'Blowfish' Password Hashing Algorithm

BCSub

A Bayesian Semiparametric Factor Analysis Model for Subtype Identification (Clustering)

bcv

Cross-Validation for the SVD (Bi-Cross-Validation)

bda

Density Estimation for Grouped Data

bde

Bounded Density Estimation

BDgraph

Bayesian Structure Learning in Graphical Models using Birth-Death MCMC

bdlp

A Package for Transparent Artificial Data Generation

bdots

Bootstrapped Differences of Time Series

bdpopt

Optimisation of Bayesian Decision Problems

bdpv

Inference and design for predictive values in binary diagnostic tests

BDR

Big Data Ready

bdrift

Beta Drift Analysis

bdscale

Remove Weekends and Holidays from ggplot2 Axes

bdsmatrix

Routines for Block Diagonal Symmetric matrices

bdsmatrix

Routines for Block Diagonal Symmetric matrices

bdvis

Biodiversity Data Visualizations

BDWreg

Bayesian Inference for Discrete Weibull Regression

bdynsys

Bayesian Dynamical System Model

BEACH

Biometric Exploratory Analysis Creation House

beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

beadarrayFilter

Bead filtering for Illumina bead arrays

beadarrayMSV

Analysis of Illumina BeadArray SNP data including MSV markers

beadarraySNP

Normalization and reporting of Illumina SNP bead arrays

BeadDataPackR

Compression of Illumina BeadArray data

beanplot

Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)

BEANSP

Bayesian Estimate of Age-specific Nest Survival Probabilities

beanz

Bayesian Analysis of Heterogeneous Treatment Effect

bea.R

Bureau of Economic Analysis API

BEAT

BEAT - BS-Seq Epimutation Analysis Toolkit

BEclear

Correct for batch effects in DNA methylation data

BEDASSLE

Quantifies effects of geo/eco distance on genetic differentiation

BEDMatrix

Matrices Backed by Binary PED Files (PLINK)

bedr

Genomic Region Processing using Tools Such as BEDtools, BEDOPS and Tabix

beepr

Easily Play Notification Sounds on any Platform

beeswarm

The Bee Swarm Plot, an Alternative to Stripchart

belex

Download Historical Data from the Belgrade Stock Exchange

benchden

28 benchmark densities from Berlinet/Devroye (1994)

benchmark

Benchmark Experiments Toolbox

Benchmarking

Benchmark and Frontier Analysis Using DEA and SFA

benchmarkme

Crowd Sourced System Benchmarks

benchmarkmeData

Data Set for the 'benchmarkme' Package

benchr

High Precise Measurement of R Expressions Execution Time

benford.analysis

Benford Analysis for Data Validation and Forensic Analytics

BenfordTests

Statistical Tests for Evaluating Conformity to Benford's Law

bentcableAR

Bent-Cable Regression for Independent Data or Autoregressive Time Series

BEQI2

Benthic Ecosystem Quality Index 2

ber

Batch Effects Removal

Bergm

Bayesian analysis for exponential random graph models

berryFunctions

Function Collection Related to Plotting and Hydrology

bertin

Bertin matrix display

Bessel

Bessel Functions Computations and Approximations

Bessel

Bessel -- Bessel Functions Computations and Approximations

BEST

Bayesian Estimation Supersedes the t-Test

bestglm

Best Subset GLM

BetaBit

Mini Games from Adventures of Beta and Bit

betafam

Detecting rare variants for quantitative traits using nuclear families

betalink

Beta-Diversity of Species Interactions

betapart

Partitioning Beta Diversity into Turnover and Nestedness Components

betapart

Partitioning Beta Diversity into Turnover and Nestedness Components

betaper

Functions to incorporate taxonomic uncertainty on multivariate analyses of ecological data

betareg

Beta Regression

betareg

Beta Regression

betas

Standardized Beta Coefficients

betategarch

Simulation, Estimation and Forecasting of Beta-Skew-t-EGARCH Models

bethel

Bethel's algorithm.

betr

Identify differentially expressed genes in microarray time-course data

BETS

Brazilian Economic Time Series

BeviMed

Bayesian Evaluation of Variant Involvement in Mendelian Disorders

beyondWhittle

Bayesian Spectral Inference for Stationary Time Series

bezier

Bezier Curve and Spline Toolkit

bfa

Bayesian Factor Analysis

bfa

Bayesian Factor Analysis

bfast

Breaks For Additive Season and Trend (BFAST)

bfast

Breaks For Additive Season and Trend

bfork

Basic Unix Process Control

bfp

Bayesian Fractional Polynomials

bfp

Bayesian Fractional Polynomials

bgafun

BGAfun A method to identify specifity determining residues in protein families

BgeeDB

Annotation and gene expression data retrieval from Bgee database

bgeva

Binary Generalized Extreme Value Additive Models

bglm

Bayesian Estimation in Generalized Linear Models

BGLR

Bayesian Generalized Linear Regression

BGLR

Bayesian Generalized Linear Regression

BGLRutils

Utilities for Bayesian Generalized Linear Regression

bgmfiles

Example BGM Files for the Atlantis Ecosystem Model

BGmix

Bayesian models for differential gene expression

bgmm

Gaussian Mixture Modeling Algorithms And The Belief-based Mixture Modeling

BGPhazard

Markov Beta and Gamma Processes for Modeling Hazard Rates

BGSIMD

Block Gibbs Sampler with Incomplete Multinomial Distribution

bgsmtr

Bayesian Group Sparse Multi-Task Regression

bgx

Bayesian Gene eXpression

BH

The Boost C++ Libraries

BH

Boost C++ Header Files

Bhat

General likelihood exploration

BHC

Bayesian Hierarchical Clustering

BHH2

Useful Functions for Box, Hunter and Hunter II

bhm

Biomarker Threshold Models

biasbetareg

Bias correction of the parameter estimates of the beta regression model

BiasedUrn

Biased Urn Model Distributions

bib2df

Parse a BibTeX File to a Tibble

BiBitR

R Wrapper for Java Implementation of BiBit

bibliometrix

Bibliometric and Co-Citation Analysis Tool

bibliospec

Reading Mass Spectrometric Search Results

bibtex

bibtex parser

bibtex

bibtex parser

BicARE

Biclustering Analysis and Results Exploration

biclust

BiCluster Algorithms

biclust

BiCluster Algorithms

biclustRank

Ranking of biclusters using another data source

BiDimRegression

Calculates the bidimensional regression between two 2D configurations

BIEN

Tools for Accessing the Botanical Ecology and Information Network Database

bifactorial

Inferences for bi- and trifactorial trial designs

bife

Binary Choice Models with Fixed Effects

BIFIEsurvey

Tools for Survey Statistics in Educational Assessment

bigalgebra

BLAS routines for native R matrices and big.matrix objects.

bigalgebra

BLAS routines for native R matrices and big.matrix objects.

biganalytics

A library of utilities for big.matrix objects of package bigmemory.

biganalytics

Utilities for 'big.matrix' Objects from Package 'bigmemory'

bigdata

Big Data Analytics

BIGDAWG

Case-Control Analysis of Multi-Allelic Loci

bigFastlm

Fast Linear Models for Objects from the 'bigmemory' Package

bigGP

Distributed Gaussian Process Calculations

BiGGR

Constraint based modeling in R using metabolic reconstruction databases

biglars

Scalable Least-Angle Regression and Lasso

biglasso

Extending Lasso Model Fitting to Big Data

biglm

bounded memory linear and generalized linear models

biglme

Procedure for doing inference of one-way Linear Mixed Effects models.

bigmelon

Illumina methylation array analysis for large experiments

bigmemory

Manage massive matrices with shared memory and memory-mapped files

bigmemory

Manage Massive Matrices with Shared Memory and Memory-Mapped Files

bigmemoryExtras

An extension of the bigmemory package with added safety, convenience, and a factor class

bigmemory.sri

A shared resource interface for Bigmemory Project packages

bigmemory.sri

A shared resource interface for Bigmemory Project packages

bigml

Bindings for the BigML API

bigmlogit

Estimation of models with limited dependent variables

bigpca

PCA, Transpose and Multicore Functionality for 'big.matrix' Objects

bigQueryR

Interface with Google BigQuery with Shiny Compatibility

BigQuic

Big Quadratic Inverse Covariance Estimation

bigReg

Generalized Linear Models (GLM) for Large Data Sets

bigrquery

An Interface to Google's 'BigQuery' 'API'

bigRR

Generalized Ridge Regression (with special advantage for p >> n cases)

bigRR

Generalized Ridge Regression (with special advantage for p >> n cases)

BigSEM

Constructing Large Systems of Structural Equations

bigsplines

Smoothing Splines for Large Samples

bigstep

Stepwise Selection for Large Data Sets

bigtabulate

Table, Apply, and Split Functionality for Matrix and 'big.matrix' Objects

bigtcr

Nonparametric Analysis of Bivariate Gap Time with Competing Risks

BigTSP

Top Scoring Pair based methods for classification

BigVAR

Dimension Reduction Methods for Multivariate Time Series

bikeshare14

Bay Area Bike Share Trips in 2014

bild

BInary Longitudinal Data

bimetallic

Power for SNP analyses using silver standard cases

bimixt

Estimates Mixture Models for Case-Control Data

BimodalIndex

The Bimodality Index

Binarize

Binarization of One-Dimensional Data

BinaryEMVS

Variable Selection for Binary Data Using the EM Algorithm

BinaryEPPM

Mean and Variance Modeling of Binary Data

binaryLogic

Binary Logic

binda

Multi-Class Discriminant Analysis using Binary Predictors

bindata

Generation of Artificial Binary Data

bindr

Parametrized Active Bindings

bindrcpp

An 'Rcpp' Interface to Active Bindings

binequality

Methods for Analyzing Binned Income Data

binford

Binford's Hunter-Gatherer Data

bingat

Binary Graph Analysis Tools

binGroup

Evaluation and experimental design for binomial group testing

binhf

Haar-Fisz functions for binomial data

binman

A Binary Download Manager

binMto

Asymptotic simultaneous confidence intervals for many-to-one comparisons of proportions

BinNonNor

Data Generation with Binary and Continuous Non-Normal Components

BinNor

Simultaneous Generation of Multivariate Binary and Normal Variates

binom

Binomial Confidence Intervals For Several Parameterizations

binom

Binomial Confidence Intervals For Several Parameterizations

binomen

'Taxonomic' Specification and Parsing Methods

binomialcftp

Generates binomial random numbers via the coupling from the past algorithm

binomlogit

Efficient MCMC for Binomial Logit Models

binomSamSize

Confidence Intervals and Sample Size Determination for a Binomial Proportion under Simple Random Sampling and Pooled Sampling

binomTools

Performing diagnostics on binomial regression models

binomTools

Performing diagnostics on binomial regression models

BinOrdNonNor

Concurrent Generation of Binary, Ordinal and Continuous Data

binr

Cut Numeric Values into Evenly Distributed Groups

binseqtest

Exact Binary Sequential Designs and Analysis

binsmooth

Generate PDFs and CDFs from Binned Data

binst

Data Preprocessing, Binning for Classification and Regression

bio3d

Biological Structure Analysis

bioassayR

Cross-target analysis of small molecule bioactivity

Biobase

Biobase: Base functions for Bioconductor

biobroom

Turn Bioconductor objects into tidy data frames

BioCalc

Bioclim Variables Calculator

bioCancer

Interactive Multi-Omics Cancers Data Visualization and Analysis

BiocCaseStudies

BiocCaseStudies: Support for the Case Studies Monograph

BiocCheck

Bioconductor-specific package checks

BiocGenerics

S4 generic functions for Bioconductor

biocGraph

Graph examples and use cases in Bioinformatics

BiocInstaller

Install/Update Bioconductor, CRAN, and github Packages

Biocomb

Feature Selection and Classification with the Embedded Validation Procedures for Biomedical Data Analysis

BiocParallel

Bioconductor facilities for parallel evaluation

BioCro

Simulation of Biomass Crops

BiocStyle

Standard styles for vignettes and other Bioconductor documents

biocViews

Categorized views of R package repositories

BiocWorkflowTools

Tools to aid the development of Bioconductor Workflow packages

Biodem

Biodemography Functions

bioDist

Different distance measures

BiodiversityR

Package for Community Ecology and Suitability Analysis

BIOdry

Multilevel Modeling of Dendroclimatical Fluctuations

BioFTF

Biodiversity Assessment Using Functional Tools

biogas

Process Biogas Data and Predict Biogas Production

biogeo

Point Data Quality Assessment and Coordinate Conversion

BioGeoBEARS

BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

biogram

N-Gram Analysis of Biological Sequences

Biograph

Explore Life Histories

bioimagetools

Some Tools for Imaging

bioinactivation

Simulation of Dynamic Microbial Inactivation

bio.infer

Predict environmental conditions from biological observations

biom

An interface package (beta) for the BIOM file format.

BioMark

Find Biomarkers in Two-Class Discrimination Problems

biomaRt

Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)

biomartr

Genomic Data Retrieval with R

BIOMASS

Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

biomformat

An interface package for the BIOM file format

BIOMOD

Ensemble platform for species distribution modeling

biomod2

Ensemble Platform for Species Distribution Modeling

biomod2

Ensemble Platform for Species Distribution Modeling

BIOM.utils

Utilities for the BIOM (Biological Observation Matrix) Format

BioMVCClass

Model-View-Controller (MVC) Classes That Use Biobase

biomvRCNS

Copy Number study and Segmentation for multivariate biological data

BioNet

Routines for the functional analysis of biological networks

bionetdata

Biological and chemical data networks

BioPET

Biomarker Prognostic Enrichment Tool

BioPhysConnectoR

BioPhysConnectoR

bioplots

Visualization of Overlapping Results with Heatmap

bioPN

Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets

BioQC

Detect tissue heterogeneity in expression profiles with gene sets

biorxivr

Search and Download Papers from the bioRxiv Preprint Server

bios2mds

From BIOlogical Sequences to MultiDimensional Scaling

BioSeqClass

Classification for Biological Sequences

biosignalEMG

Tools for Electromyogram Signals (EMG) Analysis

biosigner

Signature discovery from omics data

BioStatR

Initiation Ã la Statistique avec R

biostatUZH

Misc Tools of the Department of Biostatistics, EBPI, University of Zurich

Biostrings

String objects representing biological sequences, and matching algorithms

biosvd

Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling

biotic

Calculation of Freshwater Biotic Indices

biotools

Tools for Biometry and Applied Statistics in Agricultural Science

biovizBase

Basic graphic utilities for visualization of genomic data.

bipartite

Visualising Bipartite Networks and Calculating Some (Ecological) Indices

biplotbootGUI

Bootstrap on Classical Biplots and Clustering Disjoint Biplot

BiplotGUI

Interactive Biplots in R

BiplotGUI

Interactive Biplots in R

BIPOD

BIPOD (Bayesian Inference for Partially Observed diffusions)

birdnik

Connector for the Wordnik API

birdring

Methods to Analyse Ring Re-Encounter Data

BiRewire

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

birk

MA Birk's Functions

birta

Bayesian Inference of Regulation of Transcriptional Activity

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

bisectr

Tools to find bad commits with git bisect

BiSEp

Toolkit to Identify Candidate Synthetic Lethality

BiSeq

Processing and analyzing bisulfite sequencing data

bisoreg

Bayesian Isotonic Regression with Bernstein Polynomials

bit

A class for vectors of 1-bit booleans

bit

A Class for Vectors of 1-Bit Booleans

bit64

A S3 Class for Vectors of 64bit Integers

bit64

A S3 Class for Vectors of 64bit Integers

bitops

Bitwise Operations

BiTrinA

Binarization and Trinarization of One-Dimensional Data

bitrugs

Bayesian Inference of Transmission Routes Using Genome Sequences

BitSeq

Transcript expression inference and differential expression analysis for RNA-seq data

biVar

Bias-Variance Analysis of the Misclassification Rate

BivarP

Estimating the Parameters of Some Bivariate Distributions

bivarRIpower

Sample size calculations for bivariate longitudinal data

BivRegBLS

Tolerance Intervals and Errors-in-Variables Regressions in Method Comparison Studies

bivrp

Bivariate Residual Plots with Simulation Polygons

BivUnifBin

Generation of Bivariate Uniform Data and Its Relation to Bivariate Binary Data

biwavelet

Conduct univariate and bivariate wavelet analyses

biwavelet

Conduct Univariate and Bivariate Wavelet Analyses

biwt

Functions to compute the biweight mean vector and covariance & correlation matrices

bizdays

Business Days Calculations and Utilities

bkmr

Bayesian Kernel Machine Regression

BKPC

Bayesian Kernel Projection Classifier

blackbox

Black Box Optimization and Exploration of Parameter Space

BlakerCI

Blaker's Binomial Confidence Limits

BlandAltmanLeh

Plots (Slightly Extended) Bland-Altman Plots

blatr

Send Emails Using 'Blat' for Windows

Blaunet

Calculate and Analyze Blau Status for Measuring Social Distance

blavaan

Bayesian Latent Variable Analysis

BLCOP

Black-Litterman and copula-opinion pooling frameworks

BLCOP

Black-Litterman and Copula Opinion Pooling Frameworks

blendedLink

A New Link Function that Blends Two Specified Link Functions

blender

Analyze biotic homogenization of landscapes

blighty

United Kingdom coastlines

blima

Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.

blkbox

Data Exploration with Multiple Machine Learning Algorithms

blkergm

Fitting block ERGM given the block structure on social networks

blm

Binomial linear and linear-expit regression

blme

Bayesian Linear Mixed-Effects Models

blmeco

Data Files and Functions Accompanying the Book "Bayesian Data Analysis in Ecology using R, BUGS and Stan"

blmr

Broken Line Model Regression

blob

A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')

blockcluster

Coclustering Package for Binary, Categorical, Contingency and Continuous Data-Sets

blockDemac

parallel DEMC with several parameter blocks

blockmatrix

blockmatrix: Tools to solve algebraic systems with partitioned matrices

BlockMessage

Creates strings that show a text message in 8 by 8 block letters

blockmodeling

An R package for Generalized and classical blockmodeling of valued networks

blockmodeling

An R package for generalized and classical blockmodeling of valued networks

blockmodels

Latent and Stochastic Block Model Estimation by a 'V-EM' Algorithm

blockra

Block Rearrangement Algorithm

blockrand

Randomization for block random clinical trials

blockrand

Randomization for block random clinical trials

blocksdesign

Nested and Crossed Block Designs for Unstructured and Factorial Treatment Sets

blockseg

Two Dimensional Change-Points Detection

blockTools

Block, Assign, and Diagnose Potential Interference in Randomized Experiments

Blossom

Statistical Comparisons with Distance-Function Based Permutation Tests

blotter

Tools for Transaction-Oriented Trading Systems Development

BLR

Bayesian Linear Regression

BLR

Bayesian Linear Regression

blsAPI

Request Data from the U.S. Bureau of Labor Statistics API

blscrapeR

An API Wrapper for the Bureau of Labor Statistics (BLS)

blupsurv

Recurrent events with BLUPs

BMA

Bayesian Model Averaging

bmd

Benchmark dose analysis for dose-response data

bmem

Mediation analysis with missing data using bootstrap

bmem

Mediation analysis with missing data using bootstrap

bmeta

Bayesian Meta-Analysis and Meta-Regression

BMhyd

PCM for Hybridization

Bmix

Bayesian Sampling for Stick-Breaking Mixtures

bmixture

Bayesian Estimation for Finite Mixture of Distributions

bmk

MCMC diagnostics package

bmlm

Bayesian Multilevel Mediation

bmmix

Bayesian multinomial mixture

BMN

The pseudo-likelihood method for pairwise binary markov networks

bmp

Read Windows Bitmap (BMP) images

bmrm

Bundle Methods for Regularized Risk Minimization Package

BMRV

Bayesian Models for Rare Variant Association Analysis

BMRV

Bayesian Models for Rare Variant Association Analysis

BMS

Bayesian Model Averaging Library

BNDataGenerator

Data Generator based on Bayesian Network Model

bnlearn

Bayesian Network Structure Learning, Parameter Learning and Inference

bnnSurvival

Bagged k-Nearest Neighbors Survival Prediction

bnormnlr

Bayesian Estimation for Normal Heteroscedastic Nonlinear Regression Models

bnpa

Bayesian Networks & Path Analysis

BNPdensity

Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures

BNPMIXcluster

Bayesian Nonparametric Model for Clustering with Mixed Scale Variables

bnpmr

Bayesian monotonic nonparametric regression

BNPTSclust

A Bayesian Nonparametric Algorithm for Time Series Clustering

BNSP

Bayesian Non- and Semi-Parametric Model Fitting

bnspatial

Spatial Implementation of Bayesian Networks and Mapping

bnstruct

Bayesian Network Structure Learning from Data with Missing Values

boa

Bayesian Output Analysis Program (BOA) for MCMC

BoardGames

Board Games and Tools for Building Board Games

bodenmiller

Profilling of Peripheral Blood Mononuclear Cells using CyTOF

BOG

Bacterium and Virus Analysis of Orthologous Groups (BOG) is a Package for Identifying Differentially Regulated Genes in the Light of Gene Functions

boilerpipeR

Interface to the Boilerpipe Java Library

boilerpipeR

Interface to the boilerpipe Java library by Christian Kohlschutter (http://code.google.com/p/boilerpipe/)

BOIN

Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials

bold

Interface to Bold Systems 'API'

Bolstad

Functions for Elementary Bayesian Inference

Bolstad2

Bolstad functions

bomDataRipper

BOM data getter

BonEV

An Improved Multiple Testing Procedure for Controlling False Discovery Rates

bookdown

Authoring Books and Technical Documents with R Markdown

boolean3

Boolean Binary Response Models

BoolFilter

Optimal Estimation of Partially Observed Boolean Dynamical Systems

BoolNet

Construction, Simulation and Analysis of Boolean Networks

Boom

Bayesian Object Oriented Modeling

BoomSpikeSlab

MCMC for Spike and Slab Regression

BoostHeaders

The Boost C++ Libraries

boostmtree

Boosted Multivariate Trees for Longitudinal Data

boostr

A modular framework to bag or boost any estimation procedure.

boostSeq

Optimized GWAS cohort subset selection for resequencing studies

boot

Bootstrap Functions (Originally by Angelo Canty for S)

bootBCa

Function to find nonparametric BCa intervals

bootES

Bootstrap Effect Sizes

bootfs

Derive Robust Feature Sets for Two or Multiclass Classification Problems

bootLR

Bootstrapped Confidence Intervals for (Negative) Likelihood Ratio Tests

BootMRMR

Bootstrap-MRMR Technique for Informative Gene Selection

bootnet

Bootstrap Methods for Various Network Estimation Routines

BootPR

Bootstrap Prediction Intervals and Bias-Corrected Forecasting

bootRes

Bootstrapped Response and Correlation Functions

bootruin

A Bootstrap Test for the Probability of Ruin in the Classical Risk Process

bootspecdens

Testing equality of spectral densities

bootsPLS

Bootstrap Subsamplings of Sparse Partial Least Squares - Discriminant Analysis for Classification and Signature Identification

bootStepAIC

Bootstrap stepAIC

bootstrap

Functions for the Book "An Introduction to the Bootstrap"

bootSVD

Fast, Exact Bootstrap Principal Component Analysis for High Dimensional Data

bootTimeInference

Robust Performance Hypothesis Testing with the Sharpe Ratio

boottol

Bootstrap Tolerance Levels for Credit Scoring Validation Statistics

BootWPTOS

Test Stationarity using Bootstrap Wavelet Packet Tests

boral

Bayesian Ordination and Regression AnaLysis

Boruta

Wrapper Algorithm for All Relevant Feature Selection

BOS

Model-based clustering of multivariate ordinal data relying on a stochastic binary search algorithm

BoSSA

a Bunch of Structure and Sequence Analysis

bossMaps

Convert Binary Species Range Maps into Continuous Surfaces Based on Distance to Range Edge

bounds

Bounds for causal and sufficient-cause interactions

boussinesq

Analytic Solutions for (ground-water) Boussinesq Equation

boxoffice

Downloads Box Office Information for Given Dates (How Much Each Movie Earned in Theaters)

boxplotdbl

Double Box Plot for Two-Axes Correlation

boxr

Interface for the 'Box.com API'

bpa

Basic Pattern Analysis

bpca

Biplot of Multivariate Data Based on Principal Components Analysis

bpcp

Beta Product Confidence Procedure for Right Censored Data

bPeaks

bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes

BPEC

Bayesian Phylogeographic and Ecological Clustering

bpkde

Back-Projected Kernel Density Estimation

bpkde

Back-Projected Kernel Density Estimation

bpm

Basic functions for panel data analysis

bpp

Computations Around Bayesian Predictive Power

BPRMeth

Model higher-order methylation profiles

bptwin

Cumulative incidence models for twin data

bqtl

Bayesian QTL Mapping Toolkit

BradleyTerry2

Bradley-Terry Models

braidReports

Visualize Combined Action Response Surfaces and Report BRAID Analyses

braidrm

Fitting Dose Response with the BRAID Combined Action Model

BrailleR

Improved Access for Blind Users

BRAIN

Baffling Recursive Algorithm for Isotope distributioN calculations

brainGraph

Graph Theory Analysis of Brain MRI Data

brainR

Helper functions to misc3d and rgl packages for brain imaging

BrainStars

query gene expression data and plots from BrainStars (B*)

brainwaver

Basic wavelet analysis of multivariate time series with a visualisation and parametrisation using graph theory.

Branching

Simulation and Estimation for Branching Processes

braQCA

Bootstrapped Robustness Assessment for Qualitative Comparative Analysis

brea

Bayesian Recurrent Event Analysis

breakage

SICM pipette tip geometry estimation

breakaway

Species Richness Estimation and Modeling

breakpoint

An R Package for Multiple Break-Point Detection via the Cross-Entropy Method

breakpointError

Breakpoint detection error

bReeze

Functions for wind resource assessment

brew

Templating Framework for Report Generation

brew

Templating Framework for Report Generation

brewdata

Extracting Usable Data from the Grad Cafe Results Search

brglm

Bias reduction in binomial-response generalized linear models.

brglm

Bias reduction in binomial-response generalized linear models.

bride

Brier score decomposition of probabilistic forecasts for binary events

bride

Brier score decomposition of probabilistic forecasts for binary events

bridge

Bayesian Robust Inference for Differential Gene Expression

BridgeDbR

Code for using BridgeDb identifier mapping framework from within R

bridgedist

An Implementation of the Bridge Distribution with Logit-Link as in Wang and Louis (2003)

bridger2

Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

briskaR

Biological Risk Assessment

brm

Binary Regression Model

brms

Bayesian Regression Models using Stan

brnn

Bayesian Regularization for Feed-Forward Neural Networks

Brobdingnag

Very large numbers in R

broman

Karl Broman's R Code

broom

Convert Statistical Analysis Objects into Tidy Data Frames

brotli

A Compression Format Optimized for the Web

BrowserViz

BrowserViz: interactive R/browser graphics using websockets and JSON

BrowserVizDemo

BrowserVizDemo: How to subclass BrowserViz

brr

Bayesian Inference on the Ratio of Two Poisson Rates

brranching

Fetch 'Phylogenies' from Many Sources

BRugs

Interface to the 'OpenBUGS' MCMC Software

BSagri

Statistical methods for safety assessment in agricultural field trials

bsam

Bayesian State-Space Models for Animal Movement

BSDA

Basic Statistics and Data Analysis

bsearchtools

Binary Search Tools

BSgenome

Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation

BSGS

Bayesian Sparse Group Selection

BSGW

Bayesian Survival Model with Lasso Shrinkage Using Generalized Weibull Regression

bshazard

Nonparametric Smoothing of the Hazard Function

BsMD

Bayes Screening and Model Discrimination

bspec

Bayesian Spectral Inference

bspmma

bspmma: Bayesian Semiparametric Models for Meta-Analysis

BSquare

Bayesian Simultaneous Quantile Regression

BSSasymp

Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates

bsseq

Analyze, manage and store bisulfite sequencing data

bssn

Birnbaum-Saunders Model Based on Skew-Normal Distribution

bst

Gradient Boosting

bsts

Bayesian Structural Time Series

btb

Beyond the Border

btergm

Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood

btergm

Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood

btf

Estimates univariate function via Bayesian trend filtering

BTLLasso

Modelling Heterogeneity in Paired Comparison Data

BTR

Training and Analysing Asynchronous Boolean Models

BTSPAS

Bayesian Time-Strat. Population Analysis

btutils

Utilities for Simple Back Testing of Trading Strategies

BTYD

Implementing Buy 'Til You Die Models

BTYDplus

Probabilistic Models for Assessing and Predicting your Customer Base

BubbleTree

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

BUCSS

Bias and Uncertainty Corrected Sample Size

BufferedMatrix

A matrix data storage object held in temporary files

BufferedMatrixMethods

Microarray Data related methods that utlize BufferedMatrix objects

BUGSExamples

Collection of BUGS examples

bujar

Buckley-James Regression for Survival Data with High-Dimensional Covariates

bumphunter

Bump Hunter

bunchr

Analyze Bunching in a Kink or Notch Setting

bundesligR

All Final Tables of the Bundesliga

burnr

Advanced Fire History Analysis in R

BurStFin

Burns Statistics Financial

BurStMisc

Burns Statistics Miscellaneous

bursts

Markov model for bursty behavior in streams

BUS

Gene network reconstruction

BuyseTest

Generalized Pairwise Comparisons

bvarsv

Bayesian Analysis of a Vector Autoregressive Model with Stochastic Volatility and Time-Varying Parameters

bvenn

A Simple alternative to proportional Venn diagrams

bvls

The Stark-Parker algorithm for bounded-variable least squares

bvpSolve

Solvers for Boundary Value Problems of Differential Equations

bvpSolve

Solvers for Boundary Value Problems of Differential Equations

BVS

Bayesian Variant Selection: Bayesian Model Uncertainty Techniques for Genetic Association Studies

bvsflex

Integrative Bayesian variable selection with flexible priors

bWGR

Bagging Whole-Genome Regression

BWStest

Baumgartner Weiss Schindler Test of Equal Distributions

bytescircle

Statistics About Bytes Contained in a File as a Circle Plot

c060

Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models

c060

Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models

c212

Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)

c3net

Infering large-scale gene networks with C3NET

c3net

Infering large-scale gene networks with C3NET

C50

C5.0 Decision Trees and Rule-Based Models

C50

C5.0 Decision Trees and Rule-Based Models

ca

Simple, Multiple and Joint Correspondence Analysis

ca

Simple, Multiple and Joint Correspondence Analysis

cablecuttr

A CanIStream.It API Wrapper

cabootcrs

Bootstrap Confidence Regions for Correspondence Analysis.

cacIRT

Classification Accuracy and Consistency under Item Response Theory

CaDENCE

Conditional Density Estimation Network Construction and Evaluation

CADFtest

This package performs the CADF unit root test proposed in Hansen (1995).

CADStat

Provides a GUI to Several Statistical Methods

caesar

Encrypts and Decrypts Strings

CAFE

Chromosmal Aberrations Finder in Expression data

CAGEr

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

cAIC4

Conditional Akaike information criterion for lme4

Cairo

R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output

cairoDevice

Embeddable Cairo Graphics Device Driver

calACS

Calculations for All Common Subsequences

Calculator.LR.FNs

Calculator for LR Fuzzy Numbers

CALF

Coarse Approximation Linear Function

CALIB

Calibration model for estimating absolute expression levels from microarray data

CALIBERcodelists

Generate ICD10, Read and OPCS codelists

CALIBERdatamanage

Data Management Tools for CALIBER Datasets

CALIBERdrugdose

Extract drug dose from unstructured dosage text

CALIBERfma

R interface to the Freetext Matching Algorithm

CALIBERrfimpute

Multiple imputation using MICE and Random Forest

CALIBERrfimpute

Multiple imputation using MICE and Random Forest

calibFit

Statistical models and tools for assay calibration

calibrar

Automated Parameter Estimation for Complex (Ecological) Models

calibrate

Calibration of Scatterplot and Biplot Axes

CalibrateSSB

Weighting and Estimation for Panel Data with Non-Response

calibrator

Bayesian calibration of complex computer codes

callr

Call R from R

calmate

Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

CAM

Causal Additive Model (CAM)

CAMAN

Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN

CAMAN

Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN

camel

Calibrated Machine Learning

CAMERA

Collection of annotation related methods for mass spectrometry data

CampaR1

Trajectory Analysis

camsRad

Client for CAMS Radiation Service

camtrapR

Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

canceR

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.

cancerclass

Development and validation of diagnostic tests from high-dimensional molecular data

cancerGI

Analyses of Cancer Gene Interaction

CancerInSilico

An R interface for computational modeling of tumor progression

CancerMutationAnalysis

Cancer mutation analysis

CancerSubtypes

Cancer subtypes identification, validation and visualization based on genomic data

cancerTiming

Estimation of Temporal Ordering of Cancer Abnormalities

CAnD

Perform Chromosomal Ancestry Differences (CAnD) Analyses

CandidateBacon

Provides a measure of the average connectedness among as set of candidate genes and a network-specific distribution of the connectedness of random gene pairs for an arbitrary network of pair wise interactions.

candisc

Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis

candisc

Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis

candlesticks

Candlestick Pattern Recognition

Canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

CANSIM2R

Directly Extracts Complete CANSIM Data Tables

CANS.works

Import, manipulate and analyze data from the Massachusetts CANS tool

caOmicsV

Visualization of multi-dimentional cancer genomics data

cape

Combined Analysis of Pleiotropy and Epistasis

caper

Comparative Analyses of Phylogenetics and Evolution in R

capm

Companion Animal Population Management

captioner

Numbers Figures and Creates Simple Captions

captr

Client for the Captricity API

capushe

CAlibrating Penalities Using Slope HEuristics

capwire

Estimates population size from non-invasive sampling

car

Companion to Applied Regression

car

Companion to Applied Regression

CARBayes

Spatial Generalised Linear Mixed Models for Areal Unit Data

CARBayesdata

Data Used in the Vignettes Accompanying the CARBayes and CARBayesST Packages

CARBayesST

Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data

carcass

Estimation of the Number of Fatalities from Carcass Searches

cardidates

Identification of Cardinal Dates in Ecological Time Series

cardidates

Identification of Cardinal Dates in Ecological Time Series

Cardinal

A mass spectrometry imaging toolbox for statistical analysis

cardioModel

Cardiovascular Safety Exposure-Response Modeling in Early-Phase Clinical Studies

care

High-Dimensional Regression and CAR Score Variable Selection

CARE1

Statistical package for population size estimation in capture-recapture models.

caret

Classification and Regression Training

caret

Classification and Regression Training

caretEnsemble

Ensembles of Caret Models

caretLaTeX

LaTeX Classes for the caret Package

caribou

Estimation of caribou abundance based on large scale aggregations monitored by radio telemetry

CarletonStats

Functions for Statistics Classes at Carleton College

CARLIT

Ecological Quality Ratios Calculation and Plot

caroline

A Collection of Database, Data Structure, Visualization, and Utility Functions for R

carpenter

Build Common Tables of Summary Statistics for Reports

caRpools

CRISPR AnalyzeR for Pooled CRISPR Screens

CARrampsOcl

Reparameterized and marginalized posterior sampling for conditional autoregressive models, OpenCL implementation

cartogram

Create Cartograms with R

cartography

Thematic Cartography

carx

Censored Autoregressive Model with Exogenous Covariates

caschrono

Sries Temporelles Avec R

caseMatch

Identify Similar Cases for Qualitative Case Studies

casper

Characterization of Alternative Splicing based on Paired-End Reads

caspr

Cellular Automata for Spatial Pressure in R

cat

Analysis of categorical-variable datasets with missing values

catdap

Categorical Data Analysis Program Package

catdata

Categorical Data

CatDyn

Fishery Stock Assessment by Generalized Depletion Models

cate

High Dimensional Factor Analysis and Confounder Adjusted Testing and Estimation

Category

Category Analysis

categoryCompare

Meta-analysis of high-throughput experiments using feature annotations

catenary

Fits a Catenary to Given Points

CatEncoders

Encoders for Categorical Variables

CateSelection

Categorical Variable Selection Methods

cati

Community Assembly by Traits: Individuals and Beyond

catIrt

An R Package for Simulating IRT-Based Computerized Adaptive Tests

catlearn

Formal Modeling for Psychology

catlearn

Formal Modeling for Psychology

catnet

Categorical Bayesian Network Inference

caTools

Tools: moving window statistics, GIF, Base64, ROC AUC, etc.

catR

Generation of IRT Response Patterns under Computerized Adaptive Testing

catspec

Special models for categorical variables

causaldrf

Tools for Estimating Causal Dose Response Functions

causaleffect

Deriving Expressions of Joint Interventional Distributions and Transport Formulas in Causal Models

CausalFX

Methods for Estimating Causal Effects from Observational Data

CausalGAM

Estimation of Causal Effects with Generalized Additive Models

CausalR

Causal Reasoning Methods

causalsens

Selection Bias Approach to Sensitivity Analysis for Causal Effects

Causata

Analysis utilities for binary classification and Causata users.

CAvariants

Correspondence Analysis Variants

cba

Clustering for Business Analytics

cbmisc

Claudia's collection of miscellaneous functions

cbmodels

Collection of "combined" models: PCA-LDA, PLS-LDA, etc.

CBPS

Covariate Balancing Propensity Score

cbsodataR

Statistics Netherlands (CBS) Open Data API Client

CCA

Canonical correlation analysis

CCAGFA

Bayesian Canonical Correlation Analysis and Group Factor Analysis

ccaPP

(Robust) Canonical Correlation Analysis via Projection Pursuit

cccd

Class Cover Catch Digraphs

ccChooser

Developing a core collections

cccp

Cone Constrained Convex Problems

cccp

Cone Constrained Convex Problems

cccrm

Concordance Correlation Coefficient for Repeated (and Non-Repeated) Measures

ccda

Combined Cluster and Discriminant Analysis

ccdrAlgorithm

CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks

ccgarch

Conditional Correlation GARCH models

ccgarch2

Conditional Correlation GARCH Models

cchs

Cox Model for Case-Cohort Data with Stratified Subcohort-Selection

cclust

Convex Clustering Methods and Clustering Indexes

CCM

Correlation classification method (CCM)

ccmap

Combination Connectivity Mapping

CCMnet

Simulate Congruence Class Model for Networks

CCP

Significance Tests for Canonical Correlation Analysis (CCA)

CCpop

One and two locus GWAS of binary phenotype with case-control-population design

CCPROMISE

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

ccrepe

ccrepe_and_nc.score

CCTpack

Cultural Consensus Theory applications to data

cda

Coupled-Dipole Approximation for Electromagnetic Scattering by Three-Dimensional Clusters of Sub-Wavelength Particles

cdb

Reading and Writing Constant DataBases

cdb

Reading and Writing Constant DataBases

cdcfluview

Retrieve U.S. Flu Season Data from the CDC FluView Portal

cdcsis

Conditional Distance Correlation and Its Related Feature Screening Method

CDF.PSIdekick

Evaluate Differentially Private Algorithms for Publishing Cumulative Distribution Functions

cdfquantreg

Quantile Regression for Random Variables on the Unit Interval

CDFt

Statistical downscaling through CDF-transform

CDLasso

Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Regression

cdlTools

Tools to Download and Work with USDA Cropscape Data

CDM

Cognitive Diagnosis Modeling

CDNmoney

Components of Canadian Monetary and Credit Aggregates

cdom

R Functions to Model CDOM Spectra

CDROM

Phylogenetically Classifies Retention Mechanisms of Duplicate Genes from Gene Expression Data

cds

Constrained Dual Scaling for Detecting Response Styles

cdtRefficient

cdtRefficient

cdtRggplot2

cdtRggplot2

cdtRintroduction

cdtRintroduction

cdtRmodelling

cdtRmodelling

cdtRprogramming

cdtRprogramming

CDVine

Statistical Inference of C- And D-Vine Copulas

CEC

Cross-Entropy Clustering

cec2005benchmark

Benchmark for the CEC 2005 Special Session on Real-Parameter Optimization

cec2013

Benchmark functions for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013

CEGO

Combinatorial Efficient Global Optimization

celestial

Collection of Common Astronomical Conversion Routines and Functions

cellGrowth

Fitting cell population growth models

cellHTS

Analysis of cell-based screens

cellHTS2

Analysis of cell-based screens - revised version of cellHTS

cellity

Quality Control for Single-Cell RNA-seq Data

CellMapper

Predict genes expressed selectively in specific cell types

CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

cellranger

Translate Spreadsheet Cell Ranges to Rows and Columns

cellTree

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

CellularAutomaton

One-Dimensional Cellular Automata

cellVolumeDist

Functions to fit cell volume distributions and thereby estimate cell growth rates and division times

cellWise

Analyzing Data with Cellwise Outliers

cem

Coarsened Exact Matching

cems

Conditional Expectation Manifolds

CensMixReg

Censored Linear Mixture Regression Models

censNID

censored NID samples

censorcopula

Estimate Parameter of Bivariate Copula

censReg

Censored Regression (Tobit) Models

censReg

Censored Regression (Tobit) Models

CensRegMod

Fits Normal and Student-t Censored Regression Model

CensSpatial

Censored Spatial Models

censusGeography

Changes United States Census Geographic Code into Name of Location

censusr

Collect Data from the Census API

censys

Tools to Query the 'Censys' API

CENTIPEDE

CENTIPEDE learns a DNaseI footprint of a transcription factor and predicts its binding sites

cents

Censored time series

CEoptim

Cross-Entropy R Package for Optimization

CePa

Centrality-based pathway enrichment

CepLDA

Discriminant Analysis of Time Series in the Presence of Within-Group Spectral Variability

cepp

Context Driven Exploratory Projection Pursuit

CerioliOutlierDetection

Outlier Detection Using the Iterated RMCD Method of Cerioli (2010)

cernn

Covariance Estimation Regularized by Nuclear Norm Penalties

CexoR

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

CFAssay

Statistical analysis for the Colony Formation Assay

CFC

Cause-Specific Framework for Competing-Risk Analysis

CfEstimateQuantiles

Estimate quantiles using any order Cornish-Fisher expansion

cffdrs

Canadian Forest Fire Danger Rating System

cffdrs

Canadian Forest Fire Danger Rating System

CFL

Compensatory Fuzzy Logic

cg

Compare Groups, Analytically and Graphically

cgam

Constrained Generalized Additive Model

cgAUC

Calculate AUC-type measure when gold standard is continuous and the corresponding optimal linear combination of variables with respect to it.

cgdsr

R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)

CGEN

An R package for analysis of case-control studies in genetic epidemiology

cgenpp

Parallel genomic evaluations

cggd

Continuous Generalized Gradient Descent

cgh

Microarray CGH analysis using the Smith-Waterman algorithm

CGHbase

CGHbase: Base functions and classes for arrayCGH data analysis.

CGHcall

Calling aberrations for array CGH tumor profiles.

cghFLasso

Detecting hot spot on CGH array data with fused lasso regression.

cghMCR

Find chromosome regions showing common gains/losses

CGHnormaliter

Normalization of array CGH data with imbalanced aberrations.

CGHregions

Dimension Reduction for Array CGH Data with Minimal Information Loss.

cghseg

Segmentation Methods for Array CGH Analysis

cghseg

Segmentation methods for array CGH analysis

cgmisc

Various functions useful in computational genetics, e.g. GWAS.

CGP

Composite Gaussian process models

cgwtools

Miscellaneous Tools

CHAID

CHi-squared Automated Interaction Detection

ChainLadder

Statistical Methods and Models for Claims Reserving in General Insurance

ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

changepoint

Methods for Changepoint Detection

changepoint.np

Methods for Nonparametric Changepoint Detection

ChangepointTesting

Change Point Estimation for Clustered Signals

ChannelAttribution

Markov Model for the Online Multi-Channel Attribution Problem

ChannelAttributionApp

Shiny Web Application for the Multichannel Attribution Problem

Chaos01

0-1 Test for Chaos

ChaosGame

Chaos Game

ChargeTransport

Charge Transfer Rates and Charge Carrier Mobilities

charm

Analysis of DNA methylation data from CHARM microarrays

charmData

An example dataset for use with the charm package

CHAT

Clonal Heterogeneity Analysis Tool

CHCN

Canadian Historical Climate Network

cheb

Discrete Linear Chebyshev Approximation

chebpol

Multivariate Chebyshev Interpolation

CheckDigit

Calculate and verify check digits

checkmate

Fast and Versatile Argument Checks

checkpoint

Install Packages from Snapshots on the Checkpoint Server for Reproducibility

cheddar

Analysis and Visualisation of Ecological Communities

chemCal

Calibration Functions for Analytical Chemistry

ChemmineOB

R interface to a subset of OpenBabel functionalities

ChemmineR

Cheminformatics Toolkit for R

chemometrics

Multivariate Statistical Analysis in Chemometrics

ChemometricsWithR

Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences

ChemometricsWithRData

Data for package ChemometricsWithR

ChemoSpec

Exploratory Chemometrics for Spectroscopy

cherry

Multiple Testing Methods for Exploratory Research

CHFF

Closest History Flow Field Forecasting for Bivariate Time Series

chi

The Chi Distribution

chi2x3way

Partitioning Chi-Squared and Tau Index for Three-Way Contingency Tables

Chicago

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

childsds

Calculation of standard deviation scores adduced from different growth standards

chillR

Statistical Methods for Phenology Analysis in Temperate Fruit Trees

chimera

A package for secondary analysis of fusion products

ChIPComp

Quantitative comparison of multiple ChIP-seq datasets

chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

ChIPQC

Quality metrics for ChIPseq data

ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

chipseq

chipseq: A package for analyzing chipseq data

ChIPseqR

Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPsim

Simulation of ChIP-seq experiments

ChIPtest

Nonparametric Methods for Identifying Differential Enrichment Regions with ChIP-Seq Data

ChIPXpress

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

chngpt

Change Point Regression

CHNOSZ

Chemical Thermodynamics and Activity Diagrams

CHNOSZ

Chemical Thermodynamics and Activity Diagrams

choiceDes

Design Functions for Choice Studies

ChoiceModelR

Choice Modeling in R

choplump

Choplump tests

chopsticks

The snp.matrix and X.snp.matrix classes

chopthin

The Chopthin Resampler

chords

Estimation in Respondent Driven Samples

choroplethr

Simplify the Creation of Choropleth Maps in R

choroplethrAdmin1

Contains an Administrative-Level-1 Map of the World

choroplethrMaps

Contains maps used by the choroplethr package

chroGPS

chroGPS: visualizing the epigenome

chromatosimul

What the package does (short line)

chromDraw

chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.

chromer

Interface to Chromosome Counts Database API

ChromHeatMap

Heat map plotting by genome coordinate

chromoR

Analysis of chromosomal interactions data (correction, segmentation and comparison)

chromPlot

Global visualization tool of genomic data

chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

chron

Chronological Objects which can Handle Dates and Times

CHRONOS

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

CHsharp

Choi and Hall Style Data Sharpening

chunked

Chunkwise Text-File Processing for 'dplyr'

CIAAWconsensus

Isotope Ratio Meta-Analysis

CIDnetworks

Generative Models for Complex Networks with Conditionally Independent Dyadic Structure

CIFsmry

Weighted summary of cumulative incidence functions

cin

Causal Inference for Neuroscience

CINdex

Chromosome Instability Index

cinf

Basic tools for chemoinformatics

CINID

Curculionidae INstar IDentification

CINOEDV

Co-Information based N-Order Epistasis Detector and Visualizer

CircE

Circumplex models Estimation

circlize

Circular Visualization

CircNNTSR

Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models

CircOutlier

Detection of Outliers in Circular-Circular Regression

CircStats

Circular Statistics, from "Topics in circular Statistics" (2001)

circular

Circular Statistics

circular

Circular Statistics

cIRT

Choice Item Response Theory

cisPath

Visualization and management of the protein-protein interaction networks.

cit

Causal Inference Test

CITAN

CITation ANalysis Toolpack

CITAN

CITation ANalysis toolpack

citbcmst

CIT Breast Cancer Molecular SubTypes Prediction

citccmst

CIT Colon Cancer Molecular SubTypes Prediction

Cite

An RStudio Addin to Insert BibTex Citation in Rmarkdown Documents

CItools

Computation, comparison and sensitivity analysis of composite indicators of performance

citr

'RStudio' Add-in to Insert Markdown Citations

CityPlot

Visualization of structure and contents of a database

cjoint

AMCE Estimator for Conjoint Experiments

ckanr

Client for the Comprehensive Knowledge Archive Network ('CKAN') 'API'

Ckmeans.1d.dp

Optimal and Fast Univariate Clustering

cladoRcpp

C++ implementations of phylogenetic cladogenesis calculations

CLAG

An unsupervised non hierarchical clustering algorithm handling biological data

clamix

Clustering modal multi valued symbolic data

ClamR

Time Series Modeling for Climate Change Proxies

clarifai

Access to Clarifai API

class

Functions for Classification

ClassComparison

Classes and Methods for "Class Comparison" Problems on Microarrays

ClassDiscovery

Classes and Methods for "Class Discovery" with Microarrays or Proteomics

classGraph

Construct Graphs of S4 Class Hierarchies

classifierplots

Generates a Visualization of Classifier Performance as a Grid of Diagnostic Plots

classifly

Explore classification models in high dimensions

classify

Classification Accuracy and Consistency under IRT models.

ClassifyR

A framework for two-class classification problems, with applications to differential variability and differential distribution testing

classInt

Choose Univariate Class Intervals

classInt

Choose Univariate Class Intervals

ClassPrediction

Classes and Methods for "Class Prediction" with Microarrays or Proteomics

classSNitch

Classifies RNA Structure Change in Chemical Mapping Data

classyfire

Robust multivariate classification using highly optimised SVM ensembles

cleangeo

Cleaning Geometries from Spatial Objects

cleanNLP

A Tidy Data Model for Natural Language Processing

cleanr

Helps You to Code Cleaner

cleanUpdTSeq

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

cleaver

Cleavage of Polypeptide Sequences

clere

Simultaneous Variables Clustering and Regression

clhs

Conditioned Latin Hypercube Sampling

ClickClust

Model-Based Clustering of Categorical Sequences

clickR

Fix Data and Create Report Tables from Different Objects

clickstream

Analyzes Clickstreams Based on Markov Chains

clifro

Easily Download and Visualise Climate Data from CliFlo

clikcorr

Censoring Data and Likelihood-Based Correlation Estimation

climatol

Climate Tools (Series Homogenization and Derived Products)

climbeR

Calculate Average Minimal Depth of a Maximal Subtree for 'ranger' Package Forests

ClimClass

Climate Classification According to Several Indices

climdex.pcic

PCIC Implementation of Climdex Routines

ClimDown

Climate Downscaling Library for Daily Climate Model Output

clime

Constrained L1-minimization for Inverse (covariance) Matrix Estimation

climextRemes

Tools for Analyzing Climate Extremes

ClimMob

Crowdsourcing climate-smart agriculture

climstats

R functions for working with station and gridded climate data.

climtrends

Statistical Methods for Climate Sciences

climtrends

Statistical Methods for Climate Sciences

climwin

Climate Window Analysis

clinfun

Clinical Trial Design and Data Analysis Functions

clinsig

Clinical Significance Functions

clinUtiDNA

Clinical Utility of DNA Testing

clippda

A package for the clinical proteomic profiling data analysis

clipper

Gene Set Analysis Exploiting Pathway Topology

clipr

Read and Write from the System Clipboard

clisymbols

Unicode Symbols at the R Prompt

CLME

Constrained Inference for Linear Mixed Effects Models

clogitboost

Boosting Conditional Logit Model

clogitL1

Fitting exact conditional logistic regression with lasso and elastic net penalties.

clogitLasso

Lasso Estimation of Conditional Logistic Regression Models for Matched Case-Control Studies

Clomial

Infers clonal composition of a tumor

Clonality

Clonality testing

clonotypeR

High throughput analysis of T cell antigen receptor sequences

cloudUtil

Cloud Utilization Plots

clpAPI

R Interface to C API of COIN-OR Clp

CLSOCP

A smoothing Newton method SOCP solver

clst

Classification by local similarity threshold

clstutils

Tools for performing taxonomic assignment.

clttools

Central Limit Theorem Experiments (Theoretical and Simulation)

clubSandwich

Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections

clue

Cluster Ensembles

ClueR

CLUster Evaluation (CLUE)

clues

Clustering Method Based on Local

CluMix

Clustering and Visualization of Mixed-Type Data

clusrank

Wilcoxon Rank Sum Test for Clustered Data

clust.bin.pair

Statistical Methods for Analyzing Clustered Matched Pair Data

clustComp

Clustering Comparison Package

clustDDist

Clustering Discrete Distributions

cluster

"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.

clusterCrit

Clustering Indices

cluster.datasets

Cluster Analysis Data Sets

ClusteredMutations

Location and Visualization of Clustered Somatic Mutations

clusterExperiment

Compare clusterings for single-cell sequencing

clusterfly

Explore clustering interactively using R and GGobi

clusterGeneration

Random Cluster Generation (with Specified Degree of Separation)

clusterGenomics

Identifying clusters in genomics data by recursive partitioning

clusterhap

Clustering Genotypes in Haplotypes

Clustericat

This package performs clustering for categorical dataset.

clustering.sc.dp

Optimal Distance-Based Clustering for Multidimensional Data with Sequential Constraint

clusternomics

Integrative Clustering for Heterogeneous Biomedical Datasets

clusterpathRcpp

Fast agglomerative convex clustering, original Rcpp implementation

clusterPower

Power calculations for cluster-randomized and cluster-randomized crossover trials

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

ClusterR

Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans and K-Medoids Clustering

ClusterRankTest

Rank Tests for Clustered Data

clusterRepro

Reproducibility of gene expression clusters

clusterSEs

Calculate Cluster-Robust p-Values and Confidence Intervals

ClusterSignificance

The ClusterSignificance package provides tools to assess if clusters have a separation different from random or permuted data

clusterSim

Searching for Optimal Clustering Procedure for a Data Set

clusterStab

Compute cluster stability scores for microarray data

ClusterStability

Assessment of Stability of Individual Objects or Clusters in Partitioning Solutions

clustertend

Check the Clustering Tendency

clusteval

Evaluation of Clustering Algorithms

ClustGeo

Clustering of Observations with Geographical Constraints

clustMD

Model Based Clustering for Mixed Data

clustMixType

k-Prototypes Clustering for Mixed Variable-Type Data

ClustMMDD

Variable Selection in Clustering by Mixture Models for Discrete Data

ClustOfVar

Clustering of variables

clustRcompaR

Easy Interface for Clustering a Set of Documents and Exploring Group- Based Patterns

clustrd

Methods for Joint Dimension Reduction and Clustering

clustsig

Significant Cluster Analysis

ClustVarLV

Clustering of Variables Around Latent Variables

clustvarsel

Variable Selection for Model-Based Clustering

clv

Cluster Validation Techniques

clValid

Validation of Clustering Results

CMA

Synthesis of microarray-based classification

cmaes

Covariance Matrix Adapting Evolutionary Strategy

cmaes

Covariance Matrix Adapting Evolutionary Strategy

cmaesr

Covariance Matrix Adaptation Evolution Strategy

CMC

Cronbach-Mesbah Curve

CMF

Collective matrix factorization

cmm

Categorical Marginal Models

cmna

Computational Methods for Numerical Analysis

cMonkey

cMonkey integrated biclustering algorithm

CMPControl

Control Charts for Conway-Maxwell-Poisson Distribution

CMplot

Circle Manhattan Plot

cmprsk

Subdistribution Analysis of Competing Risks

cmprskQR

Analysis of Competing Risks Using Quantile Regressions

cmprskWeb

Multistage Competing Risks Analysis for Web data

CMRCT

Fit Capture-Mark-Recapture models in continuous time.

cmrutils

Misc Functions of the Center for the Mathematical Research

cmsaf

Tools for CM SAF NetCDF Data

cmvnorm

The Complex Multivariate Gaussian Distribution

cna

A Package for Coincidence Analysis (CNA)

cnagIO

Methods for reading CNAG files

CNAnorm

A normalization method for Copy Number Aberration in cancer samples

cncaGUI

Canonical Non-Symmetrical Correspondence Analysis in R

CNEr

CNE Detection and Visualization

cnf2freq

same Chromosome N-loci F2 frequencies

cnf2freqibdtracer

same Chromosome N-loci F2 frequencies, with IBD tracing

cn.farms

cn.FARMS - factor analysis for copy number estimation

cnmlcd

Maximum Likelihood Estimation of a Log-Concave Density Function

cn.mops

cn.mops - Mixture of Poissons for CNV detection in NGS data

CNOGpro

Copy Numbers of Genes in prokaryotes

CNORdt

Add-on to CellNOptR: Discretized time treatments

CNORfeeder

Integration of CellNOptR to add missing links

CNORfuzzy

Addon to CellNOptR: Fuzzy Logic

CNORode

ODE add-on to CellNOptR

CNPBayes

Bayesian mixture models for copy number polymorphisms

CNprep

Pre-process DNA Copy Number (CN) Data for Detection of CN Events

CNTools

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

CNVassoc

Association Analysis of CNV Data and Imputed SNPs

CNVassocData

Example data sets for association analysis of CNV data

cnvGSA

Gene Set Analysis of (Rare) Copy Number Variants

CNVPanelizer

Reliable CNV detection in targeted sequencing applications

CNVrd2

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

CNVtools

A package to test genetic association with CNV data

coala

A Framework for Coalescent Simulation

coalescentMCMC

MCMC Algorithms for the Coalescent

coalesceR

A pedagogical tool to teach the basics of coalescent theory

coarseDataTools

A Collection of Functions to Help with Analysis of Coarsely Observed Data

cobalt

Covariate Balance Tables and Plots

cobindR

Finding Co-occuring motifs of transcription factor binding sites

COBRA

Nonlinear Aggregation of Predictors

cobs

COnstrained B-Splines (Sparse Matrix Based)

cobs

COnstrained B-Splines (Sparse Matrix Based)

cobs99

Constrained B-splines -- outdated 1999 version

CoCiteStats

Different test statistics based on co-citation.

CoClust

Copula Based Cluster Analysis

COCONUT

COmbat CO-Normalization Using conTrols (COCONUT)

cocor

Comparing Correlations

cocoreg

Extracts Shared Variation in Collections of Datasets Using Regression Models

cocorresp

Co-Correspondence Analysis Methods

cocorresp

Co-correspondence analysis methods

cocron

Statistical Comparisons of Two or more Alpha Coefficients

coda

Output Analysis and Diagnostics for MCMC

codadiags

Markov chain Monte Carlo burn-in based on "bridge" statistics

cOde

Automated C Code Generation for Use with the 'deSolve' and 'bvpSolve' Packages

codebooks

Management of Survey Data

codelink

Manipulation of Codelink microarray data

codep

Multiscale Codependence Analysis

codetools

Code Analysis Tools for R

CODEX

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

codingMatrices

Alternative Factor Coding Matrices for Linear Model Formulae

codyn

Community Dynamics Metrics

coefficientalpha

Robust Cronbach's alpha with missing and non-normal data

coefficientalpha

Robust Coefficient Alpha and Omega with Missing and Non-Normal Data

coefplot

Plots Coefficients from Fitted Models

coenocliner

Coenocline Simulation

coenoflex

Gradient-Based Coenospace Vegetation Simulator

coexist

Species coexistence modeling and analysis

cofclust

Consensus Optimization Fuzzy Clustering

cofeatureR

Generate Cofeature Matrices

CoFRA

Complete Functional Regulation Analysis

CoGAPS

Coordinated Gene Activity in Pattern Sets

COGARCH

Simulation and inferenc for COGARCH(1,1) processes

COGARCH.rm

Portfolio selection with Multivariate COGARCH(p,q) models

cogena

co-expressed gene-set enrichment analysis

coGPS

cancer outlier Gene Profile Sets

COHCAP

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

CoImp

Copula Based Imputation Method

coin

Conditional Inference Procedures in a Permutation Test Framework

coin

Conditional Inference Procedures in a Permutation Test Framework

CoinMinD

Simultaneous Confidence Interval for Multinomial Proportion

cointmonitoR

Consistent Monitoring of Stationarity and Cointegrating Relationships

cointReg

Parameter Estimation and Inference in a Cointegrating Regression

cold

Count Longitudinal Data

colf

Constrained Optimization on Linear Function

CollapsABEL

Generalized CDH (GCDH) Analysis

CollocInfer

Collocation Inference for Dynamic Systems

collUtils

Auxiliary Package for Package 'CollapsABEL'

coloc

Colocalisation tests of two genetic traits

coloredICA

Implementation of Colored Independent Component Analysis and Spatial Colored Independent Component Analysis

colorfulVennPlot

Plot and add custom coloring to Venn diagrams for 2-dimensional, 3-dimensional and 4-dimensional data.

colorhcplot

Colorful Hierarchical Clustering Dendrograms

colormap

Color Palettes using Colormaps Node Module

ColorPalette

Color Palettes Generator

colorplaner

A 'ggplot2' Extension to Visualize Two Variables per Color Aesthetic Through Color Space Projections

colorRamps

Builds color tables

colorscience

Color Science Methods and Data

colorscience

Color Science Methods and Data

colorspace

Color Space Manipulation

colorspace

Color Space Manipulation

colorSpec

Color Calculations with Emphasis on Spectral Data

colortools

Tools for colors in a Hue-Saturation-Value (HSV) color model

colourlovers

R Client for the COLOURlovers API

colourpicker

A Colour Picker Tool for Shiny and for Selecting Colours in Plots

colourschemes

Data-driven colour scheme mappers

colourvision

Colour Vision Models

colr

Functions to Select and Rename Data

comato

Analysis of Concept Maps

COMBAT

A Combined Association Test for Genes using Summary Statistics

COMBIA

Synergy/Antagonism Analyses of Drug Combinations

combinat

combinatorics utilities

Combine

Game-Theoretic Probability Combination

CombinePortfolio

Estimation of Optimal Portfolio Weights by Combining Simple Portfolio Strategies

CombinePValue

Combine a Vector of Correlated p-values

CombinS

Construction Methods of some Series of PBIB Designs

combiter

Combinatorics Iterators

CombMSC

Combined Model Selection Criteria

comclim

Community climate statistics.

coMET

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

cometExactTest

Exact Test from the Combinations of Mutually Exclusive Alterations (CoMEt) Algorithm

comf

Functions for Thermal Comfort Research

ComICS

Computational Methods for Immune Cell-Type Subsets

commandr

Command pattern in R

commandr

Command pattern in R

CommEcol

Community Ecology Analyses

CommEcol

Community Ecology Analyses

commentr

Print Nicely Formatted Comments for Use in Script Files

CommonJavaJars

Useful libraries for building a Java based GUI under R

CommonJavaJars

Useful libraries for building a Java based GUI under R

commonmark

High Performance CommonMark and Github Markdown Rendering in R

CommonTrend

Extract and plot common trends from a cointegration system. Calculate P-value for Johansen Statistics.

CommT

Comparative Phylogeographic Analysis using the Community Tree Framework

COMMUNAL

Robust Selection of Cluster Number K

CommunityCorrelogram

Ecological Community Correlogram

CoModes

This package performs clustering for categorical dataset by using a conditional modes mixture model

Comp2ROC

Compare Two ROC Curves that Intersect

compactr

Creates empty plots with compact axis notation

compare

Comparing Objects for Differences

compareC

Compare Two Correlated C Indices with Right-censored Survival Outcome

CompareCausalNetworks

Interface to Diverse Estimation Methods of Causal Networks

compareDF

Do a Git Style Diff of the Rows Between Two Dataframes with Similar Structure

compareGroups

Descriptive Analysis by Groups

compareODM

comparison of medical forms in CDISC ODM format

CompareTests

Correct for Verification Bias in Diagnostic Accuracy & Agreement

comparison

Multivariate likelihood ratio calculation and evaluation

COMPASS

Combinatorial Polyfunctionality Analysis of Single Cells

compcodeR

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

compeir

Event-specific incidence rates for competing risks data

compendiumdb

Tools for Retrieval and Storage of Functional Genomics Data

compEpiTools

Tools for computational epigenomics

compete

Analyzing Social Hierarchies

CompGLM

Conway-Maxwell-Poisson GLM and distribution functions

CompGO

An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

compHclust

Complementary Hierarchical Clustering

Compind

Composite Indicators Functions

ComplexAnalysis

Numerically Evaluate Integrals and Derivatives (also Higher Order) of Vector- And Complex-Valued Functions

ComplexHeatmap

Making Complex Heatmaps

complexity

Calculate the Proportion of Permutations in Line with an Informative Hypothesis

complexplus

Functions of Complex or Real Variable

complmrob

Robust Linear Regression with Compositional Data as Covariates

CompLognormal

Functions for actuarial scientists

compoisson

Conway-Maxwell-Poisson Distribution

COMPoissonReg

Conway-Maxwell Poisson (COM-Poisson) Regression

Compositional

Compositional Data Analysis

compositions

Compositional Data Analysis

compound.Cox

Estimation, Gene Selection, and Survival Prediction Based on the Compound Covariate Method Under the Cox Proportional Hazard Model

Compounding

Computing Continuous Distributions

CompQuadForm

Distribution Function of Quadratic Forms in Normal Variables

CompR

Paired Comparison Data Analysis

CompRandFld

Composite-Likelihood Based Analysis of Random Fields

CompRandFld

Composite-Likelihood Based Analysis of Random Fields

compute.es

Compute Effect Sizes

Conake

Continuous Associated Kernel Estimation

concatenate

Human-Friendly Text from Unknown Strings

conclust

Pairwise Constraints Clustering

ConConPiWiFun

Optimisation with Continuous Convex Piecewise (Linear and Quadratic) Functions

concor

Concordance

concordance

Product Concordance

concreg

Concordance Regression

cond

Approximate conditional inference for logistic and loglinear models

condformat

Conditional Formatting in Data Frames

condGEE

Parameter estimation in conditional GEE for recurrent event gap times

conditions

Standardized Conditions for R

condmixt

Conditional Density Estimation with Neural Network Conditional Mixtures

condMVNorm

Conditional Multivariate Normal Distribution

CONDOP

Condition-Dependent Operon Predictions

CondReg

Condition Number Regularized Covariance Estimation

condSURV

Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data

condvis

Conditional Visualization for Statistical Models

coneproj

Primal or Dual Cone Projections with Routines for Constrained Regression

conf.design

Construction of factorial designs

CONFESS

Cell OrderiNg by FluorEScence Signal

confidence

Confidence Estimation of Environmental State Classifications

config

Manage Environment Specific Configuration Values

configr

An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML)

conformal

Conformal Prediction for Regression and Classification

conformal

Conformal mapping from a polygon to a disk

confreq

Configural Frequencies Analysis Using Log-Linear Modeling

confSAM

Estimates and Bounds for the False Discovery Proportion, by Permutation

conicfit

Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov

conicfit

Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov

conics

Plot Conics

Conigrave

Flexible Tools for Multiple Imputation

conjoint

Conjoint analysis package

ConjointChecks

A package to check the cancellation axioms of conjoint measurement.

connect3

A Tool for Reproducible Research by Converting 'LaTeX' Files Generated by R Sweave to Rich Text Format Files

ConnMatTools

Tools for Working with Connectivity Data

conover.test

Conover-Iman Test of Multiple Comparisons Using Rank Sums

ConR

Computation of Parameters Used in Preliminary Assessment of Conservation Status

CONS

Consonance Analysis Module

ConsensusClusterPlus

ConsensusClusterPlus

consensusSeekeR

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

ConSpline

Partial Linear Least-Squares Regression using Constrained Splines

ConsRank

Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach

constants

Defines some physical constants and functions commonly used in optics, plasmonics.

constrainedKriging

Constrained, Covariance-Matching Constrained and Universal Point or Block Kriging

ContaminatedMixt

Model-Based Clustering and Classification with the Multivariate Contaminated Normal Distribution

contfrac

Continued Fractions

contiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data

conting

Bayesian Analysis of Contingency Tables

contoureR

Contouring of Non-Regular Three-Dimensional Data

contrast

A Collection of Contrast Methods

contrast

A collection of contrast methods

controlTest

Median Comparison for Two-Sample Right-Censored Survival Data

conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

ConvCalendar

Converts dates between calendars

ConvergenceConcepts

Seeing convergence concepts in action

convert

Convert Microarray Data Objects

convertGraph

Convert Graphical Files Format

convertr

Convert Between Units

convevol

Quantifies and assesses the significance of convergent evolution

convey

Income Concentration Analysis with Complex Survey Samples

convoi

Convex Optimization in R

convoSPAT

Convolution-Based Nonstationary Spatial Modeling

cooccur

Probabilistic Species Co-Occurrence Analysis in R

cooccurNet

Co-Occurrence Network

coop

Co-Operation: Fast Covariance, Correlation, and Cosine Similarity Operations

cooptrees

Cooperative aspects of optimal trees in weighted graphs

copa

Functions to perform cancer outlier profile analysis.

copBasic

General Bivariate Copula Theory and Many Utility Functions

copCAR

Fitting the copCAR Regression Model for Discrete Areal Data

COPDSexualDimorphism

Sexual dimorphic and COPD differential analysis for gene expression and methylation.

cope

Coverage Probability Excursion (CoPE) Sets

coprimary

Sample Size Calculation for Two Primary Time-to-Event Endpoints in Clinical Trials

copula

Multivariate Dependence with Copulas

copula

Multivariate Dependence with Copulas

CopulaDTA

Copula Based Bivariate Beta-Binomial Model for Diagnostic Test Accuracy Studies

copulaedas

Estimation of Distribution Algorithms Based on Copulas

Copula.Markov

Estimation and Statistical Process Control Under Copula-Based Time Series Models

CopulaRegression

Bivariate Copula Based Regression Models

CopulaREMADA

Copula Mixed Effect Models for Bivariate and Trivariate Meta-Analysis of Diagnostic Test Accuracy Studies

CopyDetect

Computing Statistical Indices to Detect Answer Copying on Multiple-Choice Tests

copynumber

Segmentation of single- and multi-track copy number data by penalized least squares regression.

CopyNumber450k

R package for calling CNV from Illumina 450k methylation microarrays

CopyNumber450kCancer

Baseline Correction for Copy Number Data from Cancer Samples

CopywriteR

Copy number information from targeted sequencing using off-target reads

coRanking

Co-Ranking Matrix

Corbi

Collection of Rudimentary Bioinformatics Tools

Corbi

Collection of Rudimentary Bioinformatics Tools

corclass

Correlational Class Analysis

corcounts

Generate correlated count random variables

cord

Community Estimation in G-Models via CORD

cordillera

OPTICS Cordillera

CORE

Cores of Recurrent Events

CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

corehunter

Multi-Purpose Core Subset Selection

CORElearn

Classification, Regression and Feature Evaluation

coreNLP

Wrappers Around Stanford CoreNLP Tools

coreSim

Core Functionality for Simulating Quantities of Interest from Generalised Linear Models

coreTDT

TDT for compound heterozygous and recessive models

corHMM

Analysis of Binary Character Evolution

corHMM

Analysis of binary character evolution

corkscrew

Preprocessor for Data Modeling

corlink

Record Linkage, Incorporating Imputation for Missing Agreement Patterns, and Modeling Correlation Patterns Between Fields

CORM

The Clustering of Regression Models Method

Cormotif

Correlation Motif Fit

CorMut

Detect the correlated mutations based on selection pressure

coRNAi

Analysis of co-knock-down RNAi data

corpcor

Efficient Estimation of Covariance and (Partial) Correlation

corpora

Statistics and data sets for corpus frequency data

corpora

Statistics and Data Sets for Corpus Frequency Data

corr2D

Implementation of 2D Correlation Analysis in R

CorrBin

Nonparametrics with Clustered Binary and Multinomial Data

CorrBin

Nonparametrics with Clustered Binary and Multinomial Data

correctedAUC

Correcting AUC for Measurement Error

CorrectOverloadedPeaks

Correct Overloaded Peaks from GC-APCI-MS Data

CorReg

Linear Regression Based on Linear Structure Between Covariates

corregp

Functions and Methods for Correspondence Regression

Correlplot

A collection of functions for graphing correlation matrices

CORREP

Multivariate Correlation Estimator and Statistical Inference Procedures.

corrgram

Plot a Correlogram

CorrMixed

Estimate Correlations Between Repeatedly Measured Endpoints (E.g., Reliability) Based on Linear Mixed-Effects Models

corrplot

Visualization of a Correlation Matrix

corrr

Correlations in R

corrsieve

CorrSieve

CorrToolBox

Modeling Correlational Magnitude Transformations in Discretization Contexts

corTools

Tools for processing data after a Genome Wide Association Study

CoSeg

An R package for cosegregation analysis and simulating pedigrees

coseq

Co-Expression Analysis of Sequencing Data

COSINE

COndition SpecIfic sub-NEtwork

cosinor

Tools for estimating and predicting the cosinor model

cosmiq

cosmiq - COmbining Single Masses Into Quantities

cosmoFns

Functions for cosmological distances, times, luminosities, etc.

CosmoPhotoz

Photometric redshift estimation using generalized linear models

cosmosR

cosmosR

COSNet

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

cosso

Fit Regularized Nonparametric Regression Models Using COSSO Penalty.

costat

Time series costationarity determination

CosW

The CosW Distribution

cotrend

Consistant Cotrend Rank Selection

couchDB

Connect to and Work with CouchDB Databases

COUNT

Functions, Data and Code for Count Data

CountClust

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Counterfactual

Estimation and Inference Methods for Counterfactual Analysis

Countr

Flexible Univariate Count Models Based on Renewal Processes

countreg

Count Data Regression

countrycode

Convert Country Names and Country Codes

CountsEPPM

Mean and Variance Modeling of Count Data

countytimezones

Convert from UTC to Local Time for United States Counties

countyweather

Compiles Meterological Data for U.S. Counties

COUSCOus

A Residue-Residue Contact Detecting Method

covafillr

Local Polynomial Regression of State Dependent Covariates in State-Space Models

covBM

Brownian Motion Processes for 'nlme'-Models

covEB

Empirical Bayes estimate of block diagonal covariance matrices

CoverageView

Coverage visualization package for R

covLCA

Latent Class Models with Covariate Effects on Underlying and Measured Variables

covmat

Covariance Matrix Estimation

covr

Test Coverage for Packages

covreg

A simultaneous regression model for the mean and covariance

covRNA

Multivariate Analysis of Transcriptomic Data

covRobust

Robust Covariance Estimation via Nearest Neighbor Cleaning

CovSel

Model-Free Covariate Selection

CovSelHigh

Model-Free Covariate Selection in High Dimensions

covsep

Tests for Determining if the Covariance Structure of 2-Dimensional Data is Separable

covTest

Computes covariance test for adaptive linear modelling

cowplot

Streamlined Plot Theme and Plot Annotations for 'ggplot2'

cowsay

Messages, Warnings, Strings with Ascii Animals

CoxBoost

Cox models by likelihood based boosting for a single survival endpoint or competing risks

CoxFlexBoost

Boosting Flexible Cox Models (with Time-Varying Effects)

coxinterval

Cox-Type Models for Interval-Censored Data

coxme

Mixed Effects Cox Models

Coxnet

Regularized Cox Model

coxphf

Cox Regression with Firth's Penalized Likelihood

coxphw

Weighted Estimation in Cox Regression

CoxPlus

Cox Regression (Proportional Hazards Model) with Multiple Causes and Mixed Effects

CoxRidge

Cox Models with Dynamic Ridge Penalties

coxrobust

Robust Estimation in Cox Model

coxsei

Fitting a CoxSEI Model

CP

Conditional Power Calculations

cp4p

Calibration Plot for Proteomics

cpa

Confirmatory Path Analysis through the d-sep tests

CPBayes

Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations

cpca

Methods to perform Common Principal Component Analysis (CPCA)

CPE

Concordance Probability Estimates in Survival Analysis

CpGassoc

Association Between Methylation and a Phenotype of Interest

cpgen

Parallelized Genomic Prediction and GWAS

CpGFilter

CpG Filtering Method Based on Intra-class Correlation Coefficients

CPHshape

Find the maximum likelihood estimator of the shape constrained hazard baseline and the effect parameters in the Cox proportional hazards model

cpk

Clinical Pharmacokinetics

cplexAPI

R Interface to C API of IBM ILOG CPLEX

cplm

Compound Poisson Linear Models

cpm

Sequential and Batch Change Detection Using Parametric and Nonparametric Methods

CPMCGLM

Correction of the pvalue after multiple coding

Cprob

The Conditional Probability Function of a Competing Event

cpvSNP

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

cqn

Conditional quantile normalization

cqrReg

Quantile, Composite Quantile Regression and Regularized Versions

cquad

Conditional Maximum Likelihood for Quadratic Exponential Models for Binary Panel Data

CR

Power Calculation for Weighted Log-Rank Tests in Cure Rate Models

CRAC

Cosmology R Analysis Code

cRacker

R-script suite for automated processing of proteomic peptide lists

crackR

Probabilistic damage tolerance analysis for fatigue cracking of metallic aerospace structures

cramer

Multivariate nonparametric Cramer-Test for the two-sample-problem

crandatapkgs

Find Data-Only Packages on CRAN

crank

Completing Ranks

cranlogs

Download Logs from the 'RStudio' 'CRAN' Mirror

crantastic

Various R tools for http://crantastic.org/

crawl

Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data

crayon

Colored Terminal Output

crblocks

Categorical Randomized Block Data Analysis

crch

Censored Regression with Conditional Heteroscedasticity

CreditMetrics

Functions for calculating the CreditMetrics risk model

creditr

Credit Default Swaps in R

credule

Credit Default Swap Functions

cremo

cremo: Comparative REndering of Model Outputs

CRF

Conditional Random Fields

CRF

Conditional Random Fields

cricketr

Analyze Cricketers Based on ESPN Cricinfo Statsguru

CRImage

CRImage a package to classify cells and calculate tumour cellularity

crimCV

Group-Based Modelling of Longitudinal Data

crimelinkage

Statistical Methods for Crime Series Linkage

crisp

Fits a Model that Partitions the Covariate Space into Blocks in a Data- Adaptive Way

CRISPRseek

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

crisprseekplus

crisprseekplus

CrispRVariants

Tools for counting and visualising mutations in a target location

crlmm

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

CRM

Continual Reassessment Method (CRM) for Phase I Clinical Trials

crmn

CCMN and other noRMalizatioN methods for metabolomics data

crmPack

Object-Oriented Implementation of CRM Designs

crn

Downloads and Builds datasets for Climate Reference Network

crop

Graphics Cropping Tool

crop

Graphics Cropping Tool

cropData

Modelling crop trial data

cropr

simulate crop growth

CrossClustering

A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters and Identification of Outliers

crossdes

Construction of Crossover Designs

crossmatch

The Cross-match Test

crossmeta

Cross Platform Meta-Analysis of Microarray Data

Crossover

Analysis and Search of Crossover Designs

crossReg

Confidence intervals for crossover points of two simple regression lines

crosstalk

Inter-Widget Interactivity for HTML Widgets

CrossVA

Verbal Autopsy Data Transform for Use with Various Coding Algorithms

crossval

Generic Functions for Cross Validation

CrossVal

Classes and methods for cross validation of "class prediction" with microarrays or proteomics

CrossValidate

Classes and Methods for Cross Validation of "Class Prediction" with Microarrays or Proteomics

crp.CSFP

CreditRisk+ Portfolio Model

crqa

Cross-Recurrence Quantification Analysis for Categorical and Continuous Time-Series

crrp

Penalized Variable Selection in Competing Risks Regression

crrSC

Competing risks regression for Stratified and Clustered data

crrstep

Stepwise Covariate Selection for the Fine & Gray Competing Risks Regression Model

crs

Categorical Regression Splines

crskdiag

Diagnostics for Fine and Gray Model

crsnls

Nonlinear Regression Parameters Estimation by 'CRS4HC' and 'CRS4HCe'

crtests

Classification and Regression Tests

CRTgeeDR

Doubly Robust Inverse Probability Weighted Augmented GEE Estimator

CRTSize

Sample Size Estimation Functions for Cluster Randomized Trials

crul

HTTP Client

crules

Classification Rules

crunch

Crunch.io Data Tools

cruts

Interface to Climatic Research Unit Time-Series Version 3.21 Data

CrypticIBDcheck

Identifying cryptic relatedness in genetic association studies

CryptRndTest

Statistical Tests for Cryptographic Randomness

cryst

Calculate the Relative Crystallinity of Starch by XRD and FTIR

csampling

Functions for Conditional Simulation in Regression-Scale Models

CSAR

Statistical tools for the analysis of ChIP-seq data

csaw

ChIP-Seq Analysis with Windows

CSclone

Bayesian Nonparametric Modeling in R

CSFA

Connectivity Scores with Factor Analysis

cSFM

Covariate-adjusted Skewed Functional Model (cSFM)

cshapes

The CShapes Dataset and Utilities

cshapes

CShapes Dataset and Utilities

cslogistic

Conditionally Specified Logistic Regression

csn

Closed Skew-Normal Distribution

csn

Closed Skew-Normal Distribution

csound

Accessing Csound functionality through R

csp

Correlates of State Policy Data Set in R

csrplus

Methods to Test Hypotheses on the Distribution of Spatial Point Processes

csSAM

csSAM - cell-specific Significance Analysis of Microarrays

csSAM

csSAM - cell-specific Significance Analysis of Microarrays

CSSP

ChIP-Seq Statistical Power

cssTools

Cognitive Social Structure Tools

cstab

Selection of Number of Clusters via Normalized Clustering Instability

cstar

Substantive significance testing for regression estimates and marginal effects.

csvread

Fast Specialized CSV File Loader

csvy

Import and Export CSV Data with a YAML Metadata Header

ctc

Cluster and Tree Conversion.

ctglm

ctglm

cthmm

Latent Continuous Time Markov Chains

cthreshER

Continuous Threshold Expectile Regression

ctl

Correlated Trait Locus (CTL) Mapping in R

ctm

Conditional Transformation Models

CTM

A Text Mining Toolkit for Chinese Document

ctmcd

Estimating the Parameters of a Continuous-Time Markov Chain from Discrete-Time Data

ctmcmove

Modeling Animal Movement with Continuous-Time Discrete-Space Markov Chains

ctmcmove

Modeling Animal Movement with Continuous-Time Discrete-Space Markov Chains

ctmcMove

Modeling Animal Movement with Continuous-Time Discrete-Space Markov Chains

ctmDevel

Conditional Transformation Models

ctmm

Continuous-Time Movement Modeling

ctqr

Censored and Truncated Quantile Regression

cts

Continuous Time Autoregressive Models

ctsem

Continuous Time Structural Equation Modelling

ctsGE

Clustering of Time Series Gene Expression data

CTT

Classical Test Theory Functions

CTTShiny

Classical Test Theory via Shiny

ctv

CRAN Task Views

ctv

CRAN Task Views

CUB

A Class of Mixture Models for Ordinal Data

cubature

Adaptive Multivariate Integration over Hypercubes

cubfits

Codon Usage Bias Fits

Cubist

Rule- and Instance-Based Regression Modeling

Cubist

Rule- And Instance-Based Regression Modeling

CuCubes

MultiDimensional Feature Selection (MDFS)

cudaBayesreg

CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis

cudaBayesregData

Data sets for the examples used in the package "cudaBayesreg"

cudia

CUDIA Cross-level Imputation

CUFF

Charles's Utility Function using Formula

CulturalAnalytics

Functions for statistical analysis and plotting of image properties

cummeRbund

Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

CUMP

Analyze Multivariate Phenotypes by Combining Univariate Results

cumplyr

Extends ddply to allow calculation of cumulative quantities.

cumSeg

Change point detection in genomic sequences

cumstats

Cumulative Descriptive Statistics

curl

A Modern and Flexible Web Client for R

curlconverter

Tools to Transform 'cURL' Command-Line Calls to 'httr' Requests

currentSurvival

Estimation of CCI and CLFS Functions

curry

Partial Function Application with %<%, %-<%, and %><%

curve

Dynamic Systems Estimation - Curvature Extensions

curvetest

The package will formally test two curves represented by discrete data sets to be statistically equal or not when the errors of the two curves were assumed either equal or not using the tube formula to calculate the tail probabilities.

curvHDR

Filtering of Flow Cytometry Samples

cusp

Cusp-Catastrophe Model Fitting Using Maximum Likelihood

cusp

Cusp-Catastrophe Model Fitting Using Maximum Likelihood

customizedTraining

Customized Training for Lasso and Elastic-Net Regularized Generalized Linear Models

customProDB

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.

CUSUMdesign

Compute Decision Interval and Average Run Length for CUSUM Charts

cutoffR

CUTOFF: A Spatio-temporal Imputation Method

cuttlefish.model

An R package to perform LPUE standardization and stock assessment of the English Channel cuttlefish stock using a two-stage biomass model

cvAUC

Cross-Validated Area Under the ROC Curve Confidence Intervals

CVcalibration

Estimation of the Calibration Equation with Error-in Observations

CVD

Color Vision Deficiencies

CVD

Color Vision Deficiencies

CVE

Cancer Variant Explorer

cvequality

Tests for the Equality of Coefficients of Variation from Multiple Groups

cvGWAS

Genome-wide association analysis based on predictive ability

cvm.test

Discrete Cramer von Mises Goodness-of-Fit Tests

cvplogistic

Penalized Logistic Regression Model using Majorization Minimization by Coordinate Descent (MMCD) Algorithm

cvq2

Calculate the predictive squared correlation coefficient

cvrcalc

Cardiovascular Risk Calculator

CVST

Fast Cross-Validation via Sequential Testing

CVThresh

Level-Dependent Cross-Validation Thresholding

cvTools

Cross-validation tools for regression models

CVTuningCov

Regularized Estimators of Covariance Matrices with CV Tuning

cvxbiclustr

Convex Biclustering Algorithm

cvxclustr

Splitting methods for convex clustering

cwhmisc

Miscellaneous Functions for Math, Plotting, Printing, Statistics, Strings, and Tools

cwm

Cluster Weighted Models by EM algorithm

cxxfunplus

extend cxxfunction by saving the dynamic shared objects

cycle

Significance of periodic expression pattern in time-series data

cycleRtools

Tools for Cycling Data Analysis

cyclocomp

Cyclomatic Complexity of R Code

cycloids

cycloids

Cyclops

Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

cymruservices

Query 'Team Cymru' 'IP' Address, Autonomous System Number ('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware' Hash Data Services

cyphid

Cycle and Phase Identification for mastication data

cystiSim

Agent-Based Model for Taenia_solium Transmission and Control

CytobankAPI

Cytobank API Wrapper for R

cytoDiv

Cytometric diversity indices

cytofkit

cytofkit: an integrated mass cytometry data analysis pipeline

CytoML

GatingML interface for openCyto

D2C

Predicting Causal Direction from Dependency Features

d3heatmap

Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'

D3M

Two Sample Test with Wasserstein Metric

d3Network

Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R

D3partitionR

Plotting D3 Hierarchical Plots in R and Shiny

d3r

'd3.js' Utilities for R

DAAG

Data Analysis and Graphics Data and Functions

DAAGbio

Data Sets and Functions, for Demonstrations with Expression Arrays and Gene Sequences

DAAGxtras

Data Sets and Functions, supplementary to DAAG

dad

Three-Way Data Analysis Through Densities

dada2

Accurate, high-resolution sample inference from amplicon sequencing data

dae

Functions Useful in the Design and ANOVA of Experiments

daewr

Design and Analysis of Experiments with R

daewr

Design and Analysis of Experiments with R

daff

Diff, Patch and Merge for Data.frames

dafs

Data analysis for forensic scientists

dagbag

Learning directed acyclic graphs (DAGs) through bootstrap aggregating

DAGGER

Consensus genetic maps

dagitty

Graphical Analysis of Structural Causal Models

dagitty

Graphical Analysis of Structural Causal Models

dagLogo

dagLogo

dagR

R functions for directed acyclic graphs

Daim

Diagnostic accuracy of classification models.

dairy

Functions and models related to dairy production

DAISIE

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

DAKS

Data Analysis and Knowledge Spaces

DALY

The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R

dam

Data Analysis Metabolomics

daMA

Efficient design and analysis of factorial two-colour microarray data

DamiaNN

Neural Network Numerai

DAMisc

Dave Armstrong's Miscellaneous Functions

DAMisc

Dave Armstrong's Miscellaneous Functions

DAMOCLES

Dynamic Assembly Model of Colonization, Local Extinction and Speciation

dams

Dams in the United States from the National Inventory of Dams (NID)

DandEFA

Dandelion Plot for R-Mode Exploratory Factor Analysis

DanteR

Proteomics data analysis tool

DAPAR

Tools for the Differential Analysis of Proteins Abundance with R

darch

Package for Deep Architectures and Restricted Boltzmann Machines

Dark

The Analysis of Dark Adaptation Data

darksky

Tools to Work with the Dark Sky API

DART

Denoising Algorithm based on Relevance network Topology

darts

Statistical Tools to Analyze Your Darts Game

dashboard

Interactive Data Visualization with D3.js

DASiR

Distributed Annotation System in R

dat

Tools for Data Manipulation

DatABEL

File-Based Access to Large Matrices Stored on HDD in Binary Format

datacheck

Tools for Checking Data Consistency

datacheckr

Data Checking

DataClean

Data Cleaning

DataCombine

Tools for Easily Combining and Cleaning Data Sets

datadr

Divide and Recombine for Large, Complex Data

DataExplorer

Data Explorer

dataframes2xls

Write Data Frames to Xls Files

datafsm

Estimating Finite State Machine Models from Data

DataLoader

Import Multiple File Types

dataMaid

A Suite of Checks for Identification of Potential Errors in a Data Frame as Part of the Data Cleaning Process

datamap

A system for mapping foreign objects to R variables and environments

datamart

Unified access to your data sources

dataonderivatives

Easily Source Publicly Available Data on Derivatives

dataone

R Interface to the DataONE REST API

datapack

A Flexible Container to Transport and Manipulate Data and Associated Resources

datapasta

RStudio Addins for Data Copy-Pasta

dataQualityR

Performs variable level data quality checks and generates summary statistics

dataRetrieval

Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data

datarobot

DataRobot Predictive Modeling API

Dataset

Handling survey data in R. (official release)

datasets.load

Interface for Loading Datasets

Datasmith

Tools to Complete Euclidean Distance Matrices

datastepr

An Implementation of a SAS-Style Data Step

data.table

Extension of `data.frame`

data.table

Extension of data.frame

data.tree

General Purpose Hierarchical Data Structure

datautils

Support functions for packages VBmix, semisupKernelPCA, and patchPlot.

dataview

Data and Workspace Browser for Terminals

date

Functions for handling dates

date

Functions for Handling Dates

DATforDCEMRI

Deconvolution Analysis Tool for Dynamic Contrast Enhanced MRI

dave

Functions for "Data Analysis in Vegetation Ecology"

DAVIDQuery

Retrieval from the DAVID bioinformatics data resource into R

Davies

The Davies Quantile Function

dawai

Discriminant Analysis with Additional Information

dbarts

Discrete Bayesian Additive Regression Trees Sampler

DBChIP

Differential Binding of Transcription Factor with ChIP-seq

dbConnect

Provides a graphical user interface to connect with databases that use MySQL.

dbEmpLikeGOF

Goodness-of-fit and two sample comparison tests using sample entropy

dbEmpLikeNorm

Test for joint assessment of normality

DBEST

Detecting Breakpoints and Estimating Segments in Trend

dbfaker

A Tool to Ensure the Validity of Database Writes

DBGSA

methods of distance-based gene set functional enrichment analysis.

dbhydroR

'DBHYDRO' Hydrologic and Water Quality Data

DBI

R Database Interface

DBItest

Testing 'DBI' Back Ends

DBKGrad

Discrete Beta Kernel Graduation of Mortality Data

dblcens

Compute the NPMLE of distribution from doubly censored data

dbmss

Distance-Based Measures of Spatial Structures

dbscan

Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms

dbstats

Distance-Based Statistics

DCchoice

Analyzing Dichotomous Choice Contingent Valuation Data

DCchoice

Analyzing Dichotomous Choice Contingent Valuation Data

dcemri

A Package for Medical Image Analysis

dcemriS4

A Package for Image Analysis of DCE-MRI (S4 Implementation)

dcemriS4

A Package for Medical Image Analysis (S4 implementation)

DCG

Data Cloud Geometry (DCG): Using Random Walks to Find Community Structure in Social Network Analysis

DCGL

Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

dcGOR

Analysis of Ontologies and Protein Domain Annotations

dcGOR

Analysis of Ontologies and Protein Domain Annotations

dcGSA

Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles

dChipIO

Methods for Reading dChip Files

dChipIO

Methods for reading dChip files

DChIPRep

DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

DCL

Claims Reserving under the Double Chain Ladder Model

dclone

Data Cloning and MCMC Tools for Maximum Likelihood Methods

dclone

Data Cloning and MCMC Tools for Maximum Likelihood Methods

DCluster

Functions for the Detection of Spatial Clusters of Diseases

DCluster

Functions for the Detection of Spatial Clusters of Diseases

DClusterm

Model-based detection of disease clusters

DCM

Data Converter Module

dcmle

Hierarchical Models Made Easy with Data Cloning

dcmr

Attribute profile estimation using Diagnostic Classification Models and MCMC

DCODE

List Linear n-Peptide Constraints for Overlapping Protein Regions

dCovTS

Distance Covariance and Correlation for Time Series Analysis

dcv

Conventional Cross-validation statistics for climate-growth model

ddalpha

Depth-Based Classification and Calculation of Data Depth

ddCt

The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

DDD

Diversity-Dependent Diversification

ddeploy

Wrapper for the Duke Deploy REST API

ddepn

Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

ddgraph

Distinguish direct and indirect interactions with Graphical Modelling

DDHFm

Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays)

DDIwR

DDI with R

DDIwR

DDI with R

ddpcr

Analysis and Visualization of Droplet Digital PCR in R and on the Web

ddR

Distributed Data Structures in R

DDRTree

Learning Principal Graphs with DDRTree

ddst

Data Driven Smooth Tests

deadband

Statistical Deadband Algorithms Comparison

DeadCanMove

Assess how spatial roadkill patterns change with temporal sampling scheme

deal

Learning Bayesian Networks with Mixed Variables

deamer

Deconvolution density estimation with adaptive methods for a variable prone to measurement error

debias

Functions implementing MLE,its bias reduction for small samples and related issues

deBInfer

Bayesian Inference for Differential Equations

debrowser

debrowser: Interactive Differential Expresion Analysis Browser

debug

MVB's debugger for R

debug

printf-style debugging

debugme

Debug R Packages

DECIDE

DEComposition of Indirect and Direct Effects

DECIPHER

Tools for curating, analyzing, and manipulating biological sequences

decision

Statistical Decision Analysis

DecisionCurve

Calculate and Plot Decision Curves

decisionSupport

Quantitative Support of Decision Making under Uncertainty

decode

Differential Co-Expression and Differential Expression Analysis

decoder

Decode Coded Variables to Plain Text (and Vice Versa)

decomp

Various functions to quantify and decompose health inequalities

decompr

Global-Value-Chain Decomposition

decon

Deconvolution Estimation in Measurement Error Models

DeconRNASeq

Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data

deconstructSigs

Identifies Signatures Present in a Tumor Sample

deconvolveR

Empirical Bayes Estimation Strategies

DeconWK

Deconvolution by Weighted Kernels

decUpdate

Update of matrix decompositions

DEDS

Differential Expression via Distance Summary for Microarray Data

Deducer

A Data Analysis GUI for R

DeducerAlpha

Tools for aggregating scale items

DeducerANOVA

Factorial ANOVA for Deducer

DeducerExtras

Additional dialogs and functions for Deducer

DeducerPlugInExample

Deducer Plug-in Example

DeducerPlugInScaling

Reliability and factor analysis plugin

DeducerPlugInScaling

Reliability and factor analysis plugin

DeducerPSY220

PSY220 Deducer Plug-In

DeducerReshape

Converts data frames from wide to long and long to wide formats

DeducerRichOutput

Rich Output Display for Deducer

DeducerSpatial

Deducer for spatial data analysis

DeducerSpatial

Deducer for spatial data analysis

DeducerSurvival

Add Survival Dialogue to Deducer

DeducerText

Deducer GUI for Text Data

DeducerText

Deducer GUI for Text Data

deducorrect

Deductive Correction, Deductive Imputation, and Deterministic Correction

deductive

Data Correction and Imputation Using Deductive Methods

DeepBlueR

DeepBlueR

deepboost

Deep Boosting Ensemble Modeling

DeepCNV

Exploiting Normal Contamination to Infer Copy Number from Deep Sequencing

deeplearning

An Implementation of Deep Neural Network for Regression and Classification

deepnet

deep learning toolkit in R

deepnlp

Deep Learning Neural Network Models (RNN, CNN, etc) in NLP

DEEPR

Dirichlet-multinomial Evolutionary Event Profile Randomization (DEEPR) test

deepSNV

Detection of subclonal SNVs in deep sequencing data.

DEFFbinary

Compute the design effect for correlated binary data

DEFormats

Differential gene expression data formats converter

deformula

Integration of One-Dimensional Functions with Double Exponential Formulas

degenes

Detection of differentially expressed genes.

DEGraph

Two-sample tests on a graph

degreenet

Models for Skewed Count Distributions Relevant to Networks

DEGreport

Report of DEG analysis

DEGseq

Identify Differentially Expressed Genes from RNA-seq data

Delaporte

Statistical Functions for the Delaporte Distribution

deldir

Delaunay Triangulation and Dirichlet (Voronoi) Tessellation

delftfews

delftfews R extensions

DeLorean

Estimates Pseudotimes for Single Cell Expression Data

delt

Estimation of Multivariate Densities Using Adaptive Partitions

deltaGseg

deltaGseg

deltaPlotR

Identification of dichotomous differential item functioning (DIF) using Angoff's Delta Plot method

DeMAND

DeMAND

Demerelate

Functions to Calculate Relatedness on Diploid Genetic Data

DEMEtics

Evaluating the genetic differentiation between populations based on Gst and D values.

demi

Differential Expression from Multiple Indicators

deming

Deming, Thiel-Sen and Passing-Bablock Regression

DeMix

Deconvolution Models for Mixed Transcriptomes from Heterogeneous Tumor Samples

DeMixSampleData

'DeMix' Sample Data

demography

Forecasting mortality, fertility, migration and population data

demoKde

Kernel Density Estimation for Demonstration Purposes

demoniche

demoniche - spatial population dynamics

DEMOVA

DEvelopment (of Multi-Linear QSPR/QSAR) MOdels VAlidated using Test Set

dendextend

Extending 'Dendrogram' Functionality in R

dendextendRcpp

Faster Dendrogram Manipulation using 'Rcpp'

dendroextras

Extra functions to cut, label and colour dendrogram clusters

dendrometeR

Analyzing Dendrometer Data

Dendrometry

Decipher Barr & Stroud FP-15 from STX Files

DendSer

Dendrogram seriation: ordering for visualisation

dendsort

Modular Leaf Ordering Methods for Dendrogram Nodes

DengueParmEst

Parameter estimates (and real-time prediction) of a single dengue outbreak

DengueRT

Parameter Estimates and Real-Time Prediction of a Single Dengue Outbreak

DengueRT

Parameter Estimates and Real-Time Prediction of a Single Dengue Outbreak

denoiseR

Regularized Low Rank Matrix Estimation

denovolyzeR

Statistical Analyses of De Novo Genetic Variants

denpro

Visualization of Multivariate Functions, Sets, and Data

densityClust

Clustering by Fast Search and Find of Density Peaks

Density.T.HoldOut

Density.T.HoldOut: Non-combinatorial T-estimation Hold-Out for density estimation

DensParcorr

Dens-Based Method for Partial Correlation Estimation in Large Scale Brain Networks

densratio

Density Ratio Estimation

denstrip

Density strips and other methods for compactly illustrating distributions

DEoptim

Global Optimization by Differential Evolution

DEoptimR

Differential Evolution Optimization in Pure R

DEoptimR

Differential Evolution Optimization in Pure R

depend.truncation

Statistical Inference for Parametric and Semiparametric Models Based on Dependently Truncated Data

DEploid

Deconvolute Mixed Genomes with Unknown Proportions

depmix

Dependent Mixture Models

depmix

Dependent Mixture Models

depmixS4

Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4

depmixS4

Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4

depth

Nonparametric Depth Functions for Multivariate Analysis

depth.plot

Multivariate Analogy of Quantiles

depthproc

depthproc

DepthProc

Statistical Depth Functions for Multivariate Analysis

DepthProc

Statistical Depth Functions for Multivariate Analysis

depthTools

Depth Tools Package

dequer

Stacks, Queues, and 'Deques' for R

derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

derfinderHelper

derfinder helper package

derfinderPlot

Plotting functions for derfinder

Deriv

Symbolic Differentiation

derivmkts

Functions and R Code to Accompany Derivatives Markets

desc

Manipulate DESCRIPTION Files

descomponer

Seasonal Adjustment by Frequency Analysis

descr

Descriptive Statistics

DescribeDisplay

An Interface to the DescribeDisplay GGobi Plugin

describer

Describe Data in R Using Common Descriptive Statistics

descriptr

Descriptive Statistics & Distributions Exploration

DescTools

Tools for Descriptive Statistics

deseasonalize

Optimal deseasonalization for geophysical time series using AR fitting

DESeq

Differential gene expression analysis based on the negative binomial distribution

DESeq2

Differential gene expression analysis based on the negative binomial distribution

designGG

Computational tool for designing genetical genomics experiments.

designGLMM

Finding Optimal Block Designs for a Generalised Linear Mixed Model

designmatch

Construction of Optimally Matched Samples for Randomized Experiments and Observational Studies that are Balanced and Representative by Design

desiR

Desirability Functions for Ranking, Selecting, and Integrating Data

desirability

Desirabiliy Function Optimization and Ranking

desirability

Function Optimization and Ranking via Desirability Functions

desire

Desirability functions in R

desire

Desirability functions

DESnowball

Bagging with Distance-based Regression for Differential Gene Expression Analyses

deSolve

Solvers for Initial Value Problems of Differential Equations (ODE, DAE, DDE)

deSolve

Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')

DESP

Estimation of Diagonal Elements of Sparse Precision-Matrices

desplot

Plotting Field Plans for Agricultural Experiments

destiny

Creates diffusion maps

DEsubs

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

detect

Analyzing Wildlife Data with Detection Error

detect

Analyzing Wildlife Data with Detection Error

detector

Detect Data Containing Personally Identifiable Information

deTestSet

Test Set for Differential Equations

deTestSet

Test Set for Differential Equations

DetMCD

Implementation of the DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter)

DetR

Suite of Deterministic and Robust Algorithms for Linear Regression

detrendeR

Start the detrendeR Graphical User Interface (GUI)

DetSel

A computer program to detect markers responding to selection

DetSel

A computer program to detect markers responding to selection

detzrcr

Compare Detrital Zircon Suites

devEMF

EMF Graphics Output Device

Devore7

Data sets from Devore's "Prob and Stat for Eng (7th ed)"

devRate

Quantify Relationship Between Developmental Rate and Temperature in Ectotherms

devtools

Tools to Make Developing R Packages Easier

DEXSeq

Inference of differential exon usage in RNA-Seq

dexus

DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

df2json

Convert a dataframe to JSON

dfcomb

Phase I/II Adaptive Dose-Finding Design for Combination Studies

dfcrm

Dose-finding by the continual reassessment method

dfdb

Access Data Tables in a SQLite Data Base as Pseudo-Dataframes

dfdb.RODBC

Access Data Tables in an RODBC Data Base as Pseudo-Dataframes

dfexplore

Explore data.frames by plotting NA and classes of each variable

DFIT

Differential Functioning of Items and Tests

dfmta

Phase I/II Adaptive Dose-Finding Design for MTA

dfoptim

Derivative-free Optimization

dfoptim

Derivative-Free Optimization

DFP

Gene Selection

dfphase1

Phase I Control Charts (with Emphasis on Distribution-Free Methods)

dfpk

A Bayesian Dose-Finding Design using Pharmacokinetics(PK) for Phase I Clinical Trials

dga

Capture-Recapture Estimation using Bayesian Model Averaging

dGAselID

Genetic Algorithm with Incomplete Dominance for Feature Selection

DGCA

Differential Gene Correlation Analysis

dggridR

Discrete Global Grids for R

dglars

Differential Geometric LARS (dgLARS) method

dglm

Double Generalized Linear Models

dgmb

Simulating Data for PLS Mode B Structural Models

dgof

Discrete Goodness-of-Fit Tests

dgof

Discrete Goodness-of-Fit Tests

DHARMa

Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models

dhga

Differential Hub Gene Analysis

dhglm

Double Hierarchical Generalized Linear Models

dHSIC

Independence Testing via Hilbert Schmidt Independence Criterion

diagis

Diagnostic Plot and Multivariate Summary Statistics of Weighted Samples from Importance Sampling

DiagnosisMed

Diagnostic test accuracy evaluation for health professionals

diagonals

Block Diagonal Extraction or Replacement

diagram

Functions for visualising simple graphs (networks), plotting flow diagrams

diagram

Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams

DiagrammeR

Create Graph Diagrams and Flowcharts Using R

DiagrammeRsvg

Export DiagrammeR Graphviz Graphs as SVG

DiagTest3Grp

Diagnostic test summary measures for three ordinal groups

DiallelAnalysisR

Diallel Analysis with R

diaplt

Beads Summary Plot of Ranges

dice

Calculate probabilities of various dice-rolling events

DiceDesign

Designs of Computer Experiments

DiceEval

Construction and Evaluation of Metamodels

DiceKriging

Kriging Methods for Computer Experiments

DiceOptim

Kriging-Based Optimization for Computer Experiments

DiceView

Plot methods for computer experiments design and surrogate.

dichromat

Color Schemes for Dichromats

dichromat

Color Schemes for Dichromats

dicionariosIBGE

Dictionaries for reading microdata surveys from IBGE

DICOM

Import medical imaging data using the DICOM Standard

DidacticBoost

A Simple Implementation and Demonstration of Gradient Boosting

dielectric

Defines some physical constants and dielectric functions commonly used in optics, plasmonics.

DierckxSpline

R companion to "Curve and Surface Fitting with Splines"

diezeit

R Interface to the ZEIT ONLINE Content API

DIFboost

Detection of Differential Item Functioning (DIF) in Rasch Models by Boosting Techniques

Difdtl

Difference of Two Precision Matrices Estimation

DiffBind

Differential Binding Analysis of ChIP-Seq peak data

DiffCorr

Analyzing and Visualizing Differential Correlation Networks in Biological Data

diffdepprop

Calculates Confidence Intervals for two Dependent Proportions

diffEq

Functions from the book Solving Differential Equations in R

diffEq

Functions from the book Solving Differential Equations in R

diffeR

Metrics of Difference for Comparing Pairs of Maps

diffGeneAnalysis

Performs differential gene expression Analysis

diffHic

Differential Analyis of Hi-C Data

diffIRT

Diffusion IRT Models for Response and Response Time Data

DiffLogo

DiffLogo: A comparative visualisation of sequence motifs

diffloop

Identifying differential DNA loops from chromatin topology data

diffobj

Diffs for R Objects

diffr

Display Differences Between Two Files using Codediff Library

diffractometry

Baseline identification and peak decomposition for x-ray diffractograms

diffrprojects

Projects for Text Version Comparison and Analytics in R

diffrprojectswidget

Visualization for 'diffrprojects'

diffusionMap

Diffusion map

DiffusionRgqd

Inference and Analysis for Generalized Quadratic Diffusions

DiffusionRimp

Inference and Analysis for Diffusion Processes via Data Imputation and Method of Lines

DiffusionRjgqd

Inference and Analysis for Jump Generalized Quadratic Diffusions

diffusr

Network Diffusion Algorithms

DIFlasso

A Penalty Approach to Differential Item Functioning in Rasch Models

difNLR

Detection of Dichotomous Differential Item Functioning (DIF) by Non- Linear Regression Function

difR

Collection of Methods to Detect Dichotomous Differential Item Functioning (DIF)

DIFtree

Item Focused Trees for the Identification of Items in Differential Item Functioning

digest

Create Compact Hash Digests of R Objects

digest

Create cryptographic hash digests of R objects

diggit

Inference of Genetic Variants Driving Cellular Phenotypes

Digiroo2

An application programming interface for generating null models of social contacts based on individuals' space use

digitalPCR

Estimate Copy Number for Digital PCR

digitize

Use Data from Published Plots in R

digitize

digitize : a plot digitizer in R

dils

Data-Informed Link Strength. Combine multiple-relationship networks into a single weighted network. Impute (fill-in) missing network links.

DIME

DIME (Differential Identification using Mixture Ensemble)

dimRed

A Framework for Dimensionality Reduction

dina

Bayesian Estimation of DINA Model

dinamic

DiNAMIC A Method To Analyze Recurrent DNA Copy Number Aberrations in Tumors

diptest

Hartigan's Dip Test Statistic for Unimodality - Corrected

DIRECT

Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior

Directional

Directional Statistics

directlabels

Direct Labels for Multicolor Plots

directlabels

Direct labels for multicolor plots in lattice or ggplot2

Director

A dynamic visualization tool of multi-level data

directPA

Direction Analysis for Pathways and Kinases

DirectStandardisation

Adjusted Means and Proportions by Direct Standardisation

dirichlet

Dirichlet and Generalized Dirichlet Distribution functions

DirichletMultinomial

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

DirichletReg

Dirichlet Regression in R

dirmult

Estimation in Dirichlet-Multinomial distribution.

dirt

soil science related functions

Disake

Discrete associated kernel estimators

discgolf

Discourse 'API' Client

disclap

Discrete Laplace Exponential Family

disclapmix

Discrete Laplace Mixture Inference using the EM Algorithm

DiscML

DiscML: An R package for estimating evolutionary rates of discrete characters using maximum likelihood

discretecdAlgorithm

Coordinate-Descent Algorithm for Discrete Data

DiscreteInverseWeibull

Discrete Inverse Weibull Distribution

DiscreteLaplace

Discrete Laplace Distributions

discreteMTP

Multiple testing procedures for discrete test statistics

discreteRV

Create and Manipulate Discrete Random Variables

DiscreteWeibull

Discrete Weibull Distributions (Type 1 and 3)

discretization

Data preprocessing, discretization for classification.

discrimARTs

Discrimination of Alternative Reproductive Tactics (ARTs).

DiscriMiner

Tools of the Trade for Discriminant Analysis

discSurv

Discrete Time Survival Analysis

diseasemapping

Modelling Spatial Variation in Disease Risk for Areal Data

diseasemapping

Modelling Spatial Variation in Disease Risk for Areal Data

diseasemappingDevel

Functions to compliment diseasemapping

DisimForMixed

Calculate Dissimilarity Matrix for Dataset with Mixed Attributes

diskImageR

A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

dismo

Species Distribution Modeling

dismo

Species Distribution Modeling

disp2D

2D Hausdorff and Simplex Dispersion Orderings

disparityfilter

Disparity Filter Algorithm for Weighted Networks

displayHTS

displayHTS

dispmod

Dispersion models

disposables

Create Disposable R Packages for Testing

dissUtils

Utilities for making pairwise comparisons of multivariate data

Distance

Distance Sampling Detection Function and Abundance Estimation

distance.sample.size

Calculates Study Size Required for Distance Sampling

DistatisR

DiSTATIS Three Way Metric Multidimensional Scaling

distcomp

Computations over Distributed Data without Aggregation

distdrawr

Download Occurrence Data of Vascular Plants in Germany from the FLORKART Database

distfree.cr

Distribution-free confidence region (distfree.cr)

distillery

Method Functions for Confidence Intervals and to Distill Information from an Object

distory

Distance Between Phylogenetic Histories

distr

Object Oriented Implementation of Distributions

distr

Object Oriented Implementation of Distributions

distrDoc

Documentation for 'distr' Family of R Packages

distrDoc

Documentation for 'distr' Family of R Packages

distrEllipse

S4 Classes for Elliptically Contoured Distributions

distrEllipse

S4 Classes for Elliptically Contoured Distributions

distrEx

Extensions of Package 'distr'

distrEx

Extensions of Package 'distr'

DISTRIB

Four Essential Functions for Statistical Distributions Analysis: A New Functional Approach

DistributionUtils

Distribution Utilities

DistributionUtils

Distribution Utilities

distrMod

Object Oriented Implementation of Probability Models

distrMod

Object Oriented Implementation of Probability Models

distrom

Distributed Multinomial Regression

distrRmetrics

Distribution Classes for Distributions from Rmetrics

distrRmetrics

Distribution Classes for Distributions from Rmetrics

distrSim

Simulation Classes Based on Package 'distr'

distrSim

Simulation Classes Based on Package 'distr'

distrTeach

Extensions of Package 'distr' for Teaching Stochastics/Statistics in Secondary School

distrTeach

Extensions of Package 'distr' for Teaching Stochastics/Statistics in Secondary School

distrTEst

Estimation and Testing Classes Based on Package 'distr'

distrTEst

Estimation and Testing Classes Based on Package 'distr'

disttree

Trees and Forests for Distributional Regression

divagis

Provides tools for quality checks of georeferenced plant species accessions.

DivE

Diversity Estimator

diveMove

Dive Analysis and Calibration

diveMove

Dive analysis and calibration

diverse

Diversity Measures for Complex Systems

diversitree

Comparative 'Phylogenetic' Analyses of Diversification

diveRsity

A Comprehensive, General Purpose Population Genetics Analysis Package

DiversityOccupancy

Building Diversity Models from Multiple Species Occupancy Models

DiversitySampler

Functions for re-sampling a community matrix to compute diversity indices at different sampling levels.

divest

Get Images Out of DICOM Format Quickly

DivMelt

HRM Diversity Assay Analysis Tool

divo

Tools for Analysis of Diversity and Similarity in Biological Systems

dixon

Nearest Neighbour Contingency Table Analysis

DJL

Distance Measure Based Judgment and Learning

dkDNA

Diffusion Kernels on a Set of Genotypes

dks

The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.

DLASSO

Implementation of Differentiable Lasso Penalty in Linear Models

dlm

Bayesian and Likelihood Analysis of Dynamic Linear Models

dlm

Bayesian and Likelihood Analysis of Dynamic Linear Models

dlmap

Detection Localization Mapping for QTL

dlmodeler

Generalized Dynamic Linear Modeler

DLMtool

Data-Limited Methods Toolkit

dlnm

Distributed Lag Non-Linear Models

dlrm

Dynamic Linear Regression Model

dlsem

Distributed-Lag Structural Equation Modelling

dlstats

Download Stats of R Packages

dma

Dynamic Model Averaging

dml

Distance Metric Learning in R

dmm

Dyadic Mixed Model for Pedigree Data

dMod

Dynamic Modeling and Parameter Estimation in ODE Models

DMR

Delete or Merge Regressors for linear model selection.

DMRcaller

Differentially Methylated Regions caller

DMRcate

Methylation array and sequencing spatial analysis methods

DMRforPairs

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

DMRMark

DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data

dmt

Dependency Modeling Toolkit

dmt

Dependency Modeling Toolkit

DMwR

Functions and data for "Data Mining with R"

DMwR2

Functions and Data for the Second Edition of "Data Mining with R"

dna

Differential Network Analysis

DNABarcodes

A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

DNAcopy

DNA copy number data analysis

dnamatch

A procedure for large scale contamination search

DNAprofiles

DNA Profiling Evidence Analysis

DNAseqtest

Generating and Testing DNA Sequences

DNaseR

DNase I footprinting analysis of DNase-seq data

DNAshapeR

High-throughput prediction of DNA shape features

DNAtools

Tools for Analysing Forensic Genetic DNA Data

dnc

Dynamic Network Clustering

DnE

Distribution and Equation

dnet

Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

dnet

Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

DNLC

Differential Network Local Consistency Analysis

DNMF

Discriminant Non-Negative Matrix Factorization

DOBAD

Analysis of Discretely Observed Linear Birth-and-Death(-and-Immigration) Markov Chains

doBy

Groupwise Statistics, LSmeans, Linear Contrasts, Utilities

docopt

Command-Line Interface Specification Language

docopulae

Optimal Designs for Copula Models

documair

Automatic Documentation for R packages

documair

Automatic Documentation for R packages

docxtools

Tools for R Markdown to Docx Documents

docxtractr

Extract Data Tables and Comments from Microsoft Word Documents

Dodge

Functions for Acceptance Sampling Ideas originated by H.F. Dodge

DODR

Detection of Differential Rhythmicity

DoE.base

Full Factorials, Orthogonal Arrays and Base Utilities for DoE Packages

DoE.wrapper

Wrapper package for design of experiments functionality

doFuture

Foreach Parallel Adaptor using the Future API of the 'future' Package

domainsignatures

Geneset enrichment based on InterPro domain signatures

doMC

Foreach Parallel Adaptor for 'parallel'

doMC

Foreach Parallel Adaptor for 'parallel'

Dominance

ADI (Average Dominance Index), Social Network Graphs with Dual Directions, and Music Notation Graph

domino

R Console Bindings for the 'Domino Command-Line Client'

doMPI

Foreach parallel adaptor for the Rmpi package

doParallel

Foreach Parallel Adaptor for the 'parallel' Package

doParallel

Foreach Parallel Adaptor for the 'parallel' Package

doppelgangR

Identify likely duplicate samples from genomic or meta-data

DOQTL

Genotyping and QTL Mapping in DO Mice

doRedis

Foreach parallel adapter for the rredis package

doRNG

Generic Reproducible Parallel Backend for foreach Loops

doRNG

Generic Reproducible Parallel Backend for foreach Loops

DOSE

Disease Ontology Semantic and Enrichment analysis

DoseFinding

Planning and Analyzing Dose Finding Experiments

doSMP

Foreach parallel adaptor for the revoIPC package

doSNOW

Foreach Parallel Adaptor for the 'snow' Package

doSNOW

Foreach Parallel Adaptor for the 'snow' Package

dosresmeta

Performing Multivariate Dose-Response Meta-Analysis

dostats

Compute Statistics Helper Functions

DOT

Render and Export DOT Graphs in R

DoTC

Distribution of Typicality Coefficients

dotCall64

Enhanced Foreign Function Interface Supporting Long Vectors

dotenv

Load Environment Variables from '.env'

dotwhisker

Dot-and-Whisker Plots of Regression Results

DoubleCone

Test against parametric regression function

DoubleExpSeq

Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage of the Dispersion Parameter

DOvalidation

Local Linear Hazard Estimation with Do-Validated and Cross-Validated Bandwidths

Dowd

Functions Ported from 'MMR2' Toolbox Offered in Kevin Dowd's Book Measuring Market Risk

Dowd

Functions Ported from 'MMR2' Toolbox Offered in Kevin Dowd's Book Measuring Market Risk

downloader

Download Files over HTTP and HTTPS

downscale

Downscaling Species Occupancy

downscale

Downscaling Species Occupancy

downsize

A Tool to Downsize Large Workflows for Testing

dpa

Dynamic Path Approach

DPBBM

Dirichlet Process Beta-Binomial Mixture

dpcR

Digital PCR Analysis

dpeaqms

Differential Protein Expression Analysis using Quantitative Mass Spectrometry Data (dpeaqms)

dpglasso

Primal Graphical Lasso

dplR

Dendrochronology Program Library in R

dplR

Dendrochronology Program Library in R

dplRCon

Concordance for Dendroclimatology

dplyr

A Grammar of Data Manipulation

dpmixsim

Dirichlet Process Mixture model simulation for clustering and image segmentation

dpmixsim

Dirichlet Process Mixture model simulation for clustering and image segmentation

dpmr

Data Package Manager for R

DPpackage

Bayesian nonparametric modeling in R

dpqrcox

The `dpqrcox' package provides d/p/q/r functions of Coxian distributions.

dprep

Data Pre-Processing and Visualization Functions for Classification

dr

Methods for Dimension Reduction for Regression

dr

Methods for Dimension Reduction for Regression

drat

Drat R Archive Template

drawExpression

Visualising R syntax through graphics

drawExpression

Visualising R syntax through graphics

DRaWR

Discriminative Random Walk with Restart

DrBats

Data Representation: Bayesian Approach That's Sparse

drc

Analysis of Dose-Response Curves

dream

DiffeRential Evolution Adaptive Metropolis

DREGAR

Regularized Estimation of Dynamic Linear Regression in the Presence of Autocorrelated Residuals (DREGAR)

drfit

Dose-Response Data Evaluation

drgee

Doubly Robust Generalized Estimating Equations

DrillR

R Driver for Apache Drill

DRIMSeq

Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq

DRIP

Discontinuous Regression and Image Processing

DriverNet

Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

drLumi

Multiplex Immunoassays Data Analysis

drm

Regression and association models for repeated categorical data

drmdel

Dual Empirical Likelihood Inference under Density Ratio Models in the Presence of Multiple Samples

dropR

Analyze Drop Out of an Experiment or Survey

drought

Tools for Drought Modeling and Assessment

DRR

Dimensionality Reduction via Regression

drsmooth

Dose-Response Modeling with Smoothing Splines

DrugClust

Implementation of a Machine Learning Framework for Predicting Drugs Side Effects

DrugVsDisease

Comparison of disease and drug profiles using Gene set Enrichment Analysis

ds

Descriptive Statistics

dsample

Discretization-Based Direct Random Sample Generation

dsample

Discretization-Based Direct Random Sample Generation

DSBayes

Bayesian subgroup analysis in clinical trials

dse

Dynamic Systems Estimation (Time Series Package)

dse

Dynamic Systems Estimation (Time Series Package)

dse1

DSE (unbundled transition package).

dse2

DSE (unbundled transition package).

dSimer

Integration of Disease Similarity Methods

dsinr

Functions and datasets for the book "Data Science in R"

DSL

Distributed Storage and List

DSL

Distributed Storage and List

dslabs

Data Science Labs

dslice

Dynamic Slicing

dsm

Density Surface Modelling of Distance Sampling Data

dsmodels

A Language to Facilitate the Creation and Visualization of Two- Dimensional Dynamical Systems

DSpat

Spatial Modelling for Distance Sampling Data

DSS

Dispersion shrinakge for sequencing data.

DSsim

Distance Sampling Simulations

dst

Using Dempster-Shafer Theory

DstarM

Analyze Two Choice Reaction Time Data with the D*M Method

DStree

Recursive Partitioning for Discrete-Time Survival Trees

dSVA

Direct Surrogate Variable Analysis

DSviaDRM

Exploring Disease Similarity in Terms of Dysfunctional Regulatory Mechanisms

DT

A Wrapper of the JavaScript Library 'DataTables'

DTA

Dynamic Transcriptome Analysis

dtables

Simplifying Descriptive Frequencies and Statistics

DTComPair

Comparison of Binary Diagnostic Tests in a Paired Study Design

DTDA

Doubly truncated data analysis

dti

Analysis of Diffusion Weighted Imaging (DWI) Data

DTK

Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes

DTMCPack

Suite of functions related to discrete-time discrete-state Markov Chains

dtplyr

Data Table Back-End for 'dplyr'

DTR

Estimation and Comparison of Dynamic Treatment Regimes

DTRlearn

Learning Algorithms for Dynamic Treatment Regimes

DTRreg

DTR Estimation and Inference via G-Estimation, Dynamic WOLS, and Q-Learning

dtt

Discrete Trigonometric Transforms

dtw

Dynamic time warping algorithms

dtw

Dynamic Time Warping Algorithms

dtwclust

Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

dtwSat

Time-Weighted Dynamic Time Warping for Satellite Image Time Series Analysis

dualKS

Dual KS Discriminant Analysis and Classification

dualScale

Dual Scaling Analysis of Multiple Choice Data

dummies

Create dummy/indicator variables flexibly and efficiently

dummy

Automatic Creation of Dummies with Support for Predictive Modeling

dummy

A dummy package to ask R-Forge to install packages that I need

DunnettTests

Software implementation of step-down and step-up Dunnett test procedures

dunn.test

Dunn's Test of Multiple Comparisons Using Rank Sums

DupChecker

a package for checking high-throughput genomic data redundancy in meta-analysis

dupiR

Bayesian inference from count data using discrete uniform priors

dupRadar

Assessment of duplication rates in RNA-Seq datasets

dvfBm

Discrete variations of a fractional Brownian motion

DVHmetrics

Analyze Dose-Volume Histograms and Check Constraints

dvn

Access to Dataverse 3 APIs

DWD

DWD implementation based on A IPM SOCP solver

DWreg

Parametric Regression for Discrete Response

dyebias

The GASSCO method for correcting for slide-dependent gene-specific dye bias

dygraphs

Interface to 'Dygraphs' Interactive Time Series Charting Library

DYM

Did You Mean?

dyn

Time Series Regression

DynamicDistribution

Dynamically visualized probability distributions and their moments

dynamicGraph

dynamicGraph

dynamichazard

Dynamic Hazard Models using State Space Models

dynamicTreeCut

Methods for Detection of Clusters in Hierarchical Clustering Dendrograms

dynatopmodel

Implementation of the Dynamic TOPMODEL Hydrological Model

dynaTree

Dynamic Trees for Learning and Design

dynBiplotGUI

Full Interactive GUI for Dynamic Biplot in R

DynClust

Denoising and clustering for dynamical image sequence (2D or 3D)+T

dynCorr

Dynamic Correlation Package

DynDoc

Dynamic document tools

dynetNLAResistance

Resisting Neighbor Label Attack in a Dynamic Network

dynia

Fit Dynamic Intervention Model

dynlm

Dynamic Linear Regression

DynNom

Dynamic Nomograms for Linear, Generalized Linear and Proportional Hazard Models

dynOmics

Fast Fourier Transform to Identify Associations Between Time Course Omics Data

dynpanel

Dynamic Panel Data Models

dynpred

Companion Package to "Dynamic Prediction in Clinical Survival Analysis"

dynr

Dynamic Modeling in R

dynRB

Dynamic Range Boxes

dynsim

Dynamic Simulations of Autoregressive Relationships

dynsurv

Dynamic Models for Survival Data

DynTxRegime

Methods for Estimating Dynamic Treatment Regimes

DynTxRegime

Methods for Estimating Dynamic Treatment Regimes

DySeq

Functions for Dyadic Sequence Analyses

e1071

Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien

e1071

Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien

eaf

Plots of the Empirical Attainment Function

eAnalytics

Dynamic Web-Based Analytics for the Energy Industry

earlywarnings

Early Warning Signals Toolbox for Detecting Critical Transitions in Timeseries

earlywarnings

Early Warning Signals Toolbox for Detecting Critical Transitions in Timeseries

earth

Multivariate Adaptive Regression Splines

earthmovdist

Wrapper to the Emd-L1 library by Haibin Ling and Kazunori Okada

earthtones

Derive a Color Palette from a Particular Location on Earth

EasyABC

Efficient Approximate Bayesian Computation Sampling Schemes

EasyABC

Efficient Approximate Bayesian Computation Sampling Schemes

easyanova

Analysis of variance and other important complementary analyzes

easydb

Generic S3 Classes for Simple Database Interfaces

easyDes

An Easy Way to Descriptive Analysis

easyformatr

Tools for Building R Formats

EasyHTMLReport

EasyHTMLReport

EasyMARK

Utility functions for working with mark-recapture data.

easynls

Easy nonlinear model

easypackages

Easy Loading and Installing of Packages

easypower

Sample Size Estimation for Experimental Designs

easyPubMed

Search and Retrieve Scientific Publication Records from Pubmed

EasyqpcR

EasyqpcR for low-throughput real-time quantitative PCR data analysis

easyreg

Easy Regression

easyRNASeq

Count summarization and normalization for RNA-Seq data

easyrodbcaccess

Simple Database Interface for SQLite, MySQL and MS Access

easyrodbcexcel

Simple database interface for RODBC Excel.

easyrodbcmysql

Simple Database Interface for MySQL

easySdcTable

Easy Interface to the Statistical Disclosure Control Package 'sdcTable'

EasyStrata

Evaluation of stratified genome-wide association meta-analysis results

easyVerification

Ensemble Forecast Verification for Large Data Sets

eat

eat

eatData

eatData

eatDesign

eatDesign

eatDev

eatDev

eatGet

eatGet

eatModel

eatModel

eatPrep

Prepare Data for IRT Analyses

eatRep

eatRep

eatRest

eatRest

eatTools

eatTools

eatTrend

Estimate National Trends in International Large-Scale Assessments

eba

Elimination-by-Aspects Models

ebal

Entropy reweighting to create balanced samples

EBarrays

Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification

EBASS

Sample Size Calculation Method for Cost-Effectiveness Studies Based on Expected Value of Perfect Information

EbayesThresh

Empirical Bayes Thresholding and Related Methods

EBcoexpress

EBcoexpress for Differential Co-Expression Analysis

ebdbNet

Empirical Bayes Estimation of Dynamic Bayesian Networks

EBEN

Empirical Bayesian Elastic Net

ebGenotyping

Genotyping and SNP Detection using Next Generation Sequencing Data

EBglmnet

Empirical Bayesian Lasso and Elastic Net Methods for Generalized Linear Models

EBImage

DUMMY DUMMY DUMMY

EBImage

Image processing and analysis toolbox for R

ebimetagenomics

EBI Metagenomics Portal

ebimetagenomics

EBI Metagenomics Portal

EBMAforecast

Ensemble BMA Forecasting

EBrank

Empirical Bayes Ranking

EBS

Exact Bayesian Segmentation

EBS

Exact Bayesian Segmentation

EBSEA

Exon Based Strategy for Expression Analysis of genes

EBSeq

An R package for gene and isoform differential expression analysis of RNA-seq data

EBSeqHMM

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

ebSNP

Genotyping and SNP calling using single-sample next generation sequencing data

ecb

Programmatic Access to the European Central Bank's Statistical Data Warehouse (SDW)

ECctmc

Simulation from Endpoint-Conditioned Continuous Time Markov Chains

ecd

Elliptic Distribution and Lambda Option Pricing Model

Ecdat

Data Sets for Econometrics

Ecdat

Data Sets for Econometrics

ecdfHT

Empirical CDF for Heavy Tailed Data

ecespa

Functions for Spatial Point Pattern Analysis

Ecfun

Functions for Ecdat

Ecfun

Functions for Ecdat

ECharts2Shiny

Embedding Interactive Charts Generated with ECharts Library into Shiny Applications

ecipex

Efficient calculation of fine structure isotope patterns via Fourier transforms of simplex-based elemental models

ecm

Build Error Correction Models

eco

Ecological Inference in 2x2 Tables

ecodist

Dissimilarity-based functions for ecological analysis

ecoengine

Programmatic Interface to the API Serving UC Berkeley's Natural History Data

EcoGenetics

Spatial Analysis of Phenotypic, Genotypic and Environmental Data

EcoHydRology

A community modeling foundation for Eco-Hydrology.

ecolitk

Meta-data and tools for E. coli

ecolMod

"A practical guide to ecological modelling - using R as a simulation platform"

ecolMod

"A Practical Guide to Ecological Modelling - Using R as a Simulation Platform"

ecomodtools

Ecological Modelling Toolbox

EconDemand

General Analysis of Various Economics Demand Systems

ecoPD

Ecologically-informed phylodiversity metrics

ecoreg

Ecological Regression using Aggregate and Individual Data

ecoretriever

R Interface to the EcoData Retriever

ecoseries

An R Interface to Brazilian Central Bank and Sidra APIs and the IPEA Data

ecosim

Toolbox for Aquatic Ecosystem Modeling

EcoSimR

Null Model Analysis for Ecological Data

ECOSolveR

Embedded Conic Solver in R

ecospace

Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

ecospat

Spatial Ecology Miscellaneous Methods

ecotoxicology

Methods for Ecotoxicology

ecotoxicology

Methods for Ecotoxicology

EcoTroph

EcoTroph R package

ecoval

Procedures for Ecological Assessment of Surface Waters

EcoVirtual

Simulation of Ecological Models

ecp

Non-Parametric Multiple Change-Point Analysis of Multivariate Data

ECPaysage

A set of R resources to teach landscape ecology, landscape analysis and spatial statistics

ecr

Evolutionary Computing in R

edarf

Exploratory Data Analysis using Random Forests

EDASeq

Exploratory Data Analysis and Normalization for RNA-Seq

edcc

Economic Design of Control Charts

edci

Edge Detection and Clustering in Images

edd

expression density diagnostics

EDDA

Experimental Design in Differential Abundance analysis

edeaR

Exploratory and Descriptive Event-Based Data Analysis

edeR

Email Data Extraction Using R

edesign

Maximum Entropy Sampling

edf

Read Data from European Data Format (EDF and EDF+) Files

EDFIR

Estimating Discrimination Factors

edfReader

Reading EDF(+) and BDF(+) Files

edfun

Creating Empirical Distribution Functions

edgar

Platform for EDGAR Filing Management

edge

Extraction of Differential Gene Expression

edgebundleR

Circle Plot with Bundled Edges

edgeCorr

Spatial Edge Correction

edgeR

Empirical Analysis of Digital Gene Expression Data in R

edgeRun

More Powerful Unconditional Testing of Negative Binomial Means for Digital Gene Expression Data

EDISON

Network Reconstruction and Changepoint Detection

EditImputeCont

Simultaneous Edit-Imputation for Continuous Microdata

editrules

Parsing, Applying, and Manipulating Data Cleaning Rules

eDMA

Dynamic Model Averaging with Grid Search

edpcr

Performs Extended Digital PCR Analysis

EDR

Estimation of the Effective Dimension Reduction ('EDR') Space

edrGraphicalTools

Provides tools for dimension reduction methods

edstan

Stan Models for Item Response Theory

eechidna

Exploring Election and Census Highly Informative Data Nationally for Australia

eefAnalytics

Analytical Package for Analysing Education Trials

eefMLM

Analytical Package for Analysing Education Trials

eegAnalysis

Tools for analysis and classification of electroencephalography (EEG) data.

eegc

Engineering Evaluation by Gene Categorization (eegc)

eegkit

Toolkit for Electroencephalography Data

eegkitdata

Data for package eegkit

eel

Extended Empirical Likelihood

EEM

Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data

eemR

Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence Data

eeptools

Convenience Functions for Education Data

EFAutilities

Utility Functions for Exploratory Factor Analysis

EFDR

Wavelet-Based Enhanced FDR for Signal Detection in Noisy Images

effectFusion

Bayesian Effect Fusion for Categorical Predictors

EffectLiteR

Average and Conditional Effects

effects

Effect Displays for Linear, Generalized Linear, and Other Models

effects

Effect Displays for Linear, Generalized Linear, and Other Models

EffectsRelBaseline

Test changes of a grouped response relative to baseline.

EffectStars

Visualization of Categorical Response Models

EffectStars2

Effect Stars

EffectTreat

Prediction of Therapeutic Success

EfficientMaxEigenpair

Efficient Initials for Computing the Maximal Eigenpair

efflog

The Causal Effects for a Causal Loglinear Model

efflog

The causal effects for a causal loglinear model

effsize

Efficient Effect Size Computation

efreadr

Read European Fluxes CSV Files

EFS

Tool for Ensemble Feature Selection

ega

Error Grid Analysis

EGAD

Extending guilt by association by degree

egcm

Engle-Granger Cointegration Models

eggCounts

Hierarchical Modelling of Faecal Egg Counts

egonet

Tool for ego-centric measures in Social Network Analysis

EGRET

Exploration and Graphics for RivEr Trends (EGRET)

EGRETci

Exploration and Graphics for RivEr Trends (EGRET) Confidence Intervals

EGSEA

Ensemble of Gene Set Enrichment Analyses

eha

Event History Analysis

eHOF

Extended HOF (Huisman-Olff-Fresco) Models

ei

Ecological Inference

EIAdata

R Wrapper for the Energy Information Administration (EIA) API

eiCompare

Compares EI, Goodman, RxC Estimates

eigeninv

Generates (dense) matrices that have a given set of eigenvalues

eigenmodel

Semiparametric factor and regression models for symmetric relational data

eigenprcomp

Computes confidence intervals for principal components

EILA

Efficient Inference of Local Ancestry

eiPack

eiPack: Ecological Inference and Higher-Dimension Data Management

eiR

Accelerated similarity searching of small molecules

eisa

Expression data analysis via the Iterative Signature Algorithm

eive

An algorithm for reducing errors-in-variable bias in simple linear regression

eiwild

Ecological Inference with individual and aggregate data

eiwild

Ecological Inference with individual and aggregate data

EL

Two-sample Empirical Likelihood

elasso

Enhanced Least Absolute Shrinkage and Selection Operator Regression Model

elastic

General Purpose Interface to 'Elasticsearch'

elasticIsing

Ising Network Estimation using Elastic Net and k-Fold Cross-Validation

elasticnet

Elastic-Net for Sparse Estimation and Sparse PCA

elasticsearchr

A Lightweight Interface for Interacting with Elasticsearch from R

ELBOW

ELBOW - Evaluating foLd change By the lOgit Way

elec

Collection of functions for statistical election audits

elec.strat

Functions for election audits using stratified random samples

electionsBR

R Functions to Download and Clean Brazilian Electoral Data

electricity

Electricity market models

electronics

Electronics

elementR

A Shiny Application for Reducing Elemental LA-ICPMS Data from Solid Structures

ElemStatLearn

Data Sets, Functions and Examples from the Book: "The Elements of Statistical Learning, Data Mining, Inference, and Prediction" by Trevor Hastie, Robert Tibshirani and Jerome Friedman

elexr

Load Associated Press Election Results with Elex

elhmc

Sampling from a Empirical Likelihood Bayesian Posterior of Parameters Using Hamiltonian Monte Carlo

elliplot

Ellipse Summary Plot of Quantiles

ellipse

Functions for drawing ellipses and ellipse-like confidence regions

elliptic

Elliptic Functions

ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

elmNN

Implementation of ELM (Extreme Learning Machine ) algorithm for SLFN ( Single Hidden Layer Feedforward Neural Networks )

ELMR

Extreme Machine Learning (ELM)

EloChoice

Preference Rating for Visual Stimuli Based on Elo Ratings

EloRating

Animal Dominance Hierarchies by Elo Rating

elrm

Exact Logistic Regression via MCMC

elsa

Entropy-based Local indicator of Spatial Association

ElstonStewart

Elston-Stewart Algorithm

ELT

Experience Life Tables

ELYP

Empirical Likelihood Analysis for the Cox Model and Yang-Prentice (2005) Model

EMA

Easy Microarray Data Analysis

EMbC

Expectation-Maximization Binary Clustering

embryogrowth

Tools to Analyze the Thermal Reaction Norm of Embryo Growth

EMC

Evolutionary Monte Carlo (EMC) algorithm

EMCluster

EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution

EMD

Empirical Mode Decomposition and Hilbert Spectral Analysis

emdbook

Support Functions and Data for "Ecological Models and Data"

emdi

Estimating and Mapping Disaggregated Indicators

emdist

Earth Mover's Distance

EMDomics

Earth Mover's Distance for Differential Analysis of Genomics Data

emg

Exponentially Modified Gaussian (EMG) Distribution

emil

Evaluation of Modeling without Information Leakage

emIRT

EM Algorithms for Estimating Item Response Theory Models

emissions

What the package does (short line)

EmiStatR

Estimation of Wastewater Emissions in Combined Sewer Systems

EML

Read and Write Ecological Metadata Language Files

EMLasso

Fit (logistic) LASSO when there is missing data in the predictors

eMLEloglin

Fitting log-Linear Models in Sparse Contingency Tables

emma

Evolutionary model-based multiresponse approach

EMMAgeo

End-Member Modelling of Grain-Size Data

emme2

Read and Write to an EMME/2 databank

EMMIXcontrasts

Contrasts in mixed effects for EMMIX model with random effects.

EMMIXskew

The EM Algorithm and Skew Mixture Distribution

EMMIXuskew

Fitting Unrestricted Multivariate Skew t Mixture Models

EMMLi

A Maximum Likelihood Approach to the Analysis of Modularity

EMMREML

Fitting Mixed Models with Known Covariance Structures

emoa

Evolutionary Multiobjective Optimization Algorithms

emojifont

Emoji and Font Awesome in Graphics

emon

Tools for Environmental and Ecological Survey Design

emon

Tools for Environmental and Ecological Survey Design

emov

Eye Movement Analysis Package for Fixation and Saccade Detection

EMP

Expected Maximum Profit Classification Performance Measure

EmpiricalBrownsMethod

Uses Brown's method to combine p-values from dependent tests

EmpiricalCalibration

Routines for Performing Empirical Calibration of Observational Study Estimates

empiricalFDR.DESeq2

Simulation-Based False Discovery Rate in RNA-Seq

emplik

Empirical Likelihood Ratio for Censored/Truncated Data

emplik2

Empirical Likelihood Ratio Test for Two Samples with Censored Data

EMSaov

The Analysis of Variance with EMS

EMSC

Extended Multiplicative Signal Correction

EMT

Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate data

emulator

Bayesian emulation of computer programs

emuR

Main Package of the EMU Speech Database Management System

EMVC

Entropy Minimization over Variable Clusters (EMVC)

enaR

Tools for Ecological Network Analysis

ENCODExplorer

A compilation of ENCODE metadata

endogenous

Classical Simultaneous Equation Models

endogMNP

R Package for Fitting Multinomial Probit Models with Endogenous Selection

endorse

R Package for Analyzing Endorsement Experiments

endtoend

Transmissions and Receptions in an End to End Network

energy

E-Statistics: Multivariate Inference via the Energy of Data

energyr

Data Published by the United States Federal Energy Regulatory Commission

english

Translate Integers into English

EngrExpt

Data sets from "Introductory Statistics for Engineering Experimentation"

EngrExpt

Data sets from "Introductory Statistics for Engineering Experimentation"

engsoccerdata

English and European Soccer Results 1871-2016

enigma

Client for the 'Enigma' 'API'

ENiRG

Ecological Niche in R and GRASS

ENMeval

Automated Runs and Evaluations of Ecological Niche Models

ENmisc

Neuwirth miscellaneous

ENmix

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

enpls

Ensemble Partial Least Squares Regression

EnQuireR

A package dedicated to questionnaires

EnQuireR

A package dedicated to questionnaires

enRich

An R Package for the Analysis of Multiple ChIP-Seq Data

EnrichedHeatmap

Making Enriched Heatmaps

EnrichmentBrowser

Seamless navigation through combined results of set-based and network-based enrichment analysis

enrichvs

Enrichment assessment of virtual screening approaches

enrichwith

Methods to Enrich R Objects with Extra Components

ensbiascoR

Resampling bias correction for large initial condition ensembles

EnsCat

Clustering of Categorical Data

ensembldb

Utilities to create and use an Ensembl based annotation database

EnsembleBase

Extensible Package for Parallel, Batch Training of Base Learners for Ensemble Modeling

ensembleBMA

Probabilistic Forecasting using Ensembles and Bayesian Model Averaging

EnsembleCV

Extensible Package for Cross-Validation-Based Integration of Base Learners

ensembleMOS

Ensemble Model Output Statistics

EnsemblePCReg

Extensible Package for Principal-Component-Regression-Based Heterogeneous Ensemble Meta-Learning

EnsemblePenReg

Extensible Classes and Methods for Penalized-Regression-Based Integration of Base Learners

ensembleR

Ensemble Models in R

ensemblVEP

R Interface to Ensembl Variant Effect Predictor

ensurer

Ensure Values at Runtime

entropart

Entropy Partitioning to Measure Diversity

entropy

Estimation of Entropy, Mutual Information and Related Quantities

EntropyEstimation

Estimation of Entropy and Related Quantities

EntropyExplorer

Tools for Exploring Differential Shannon Entropy, Differential Coefficient of Variation and Differential Expression

EnvCpt

Detection of Structural Changes in Climate and Environment Time Series

enveomics.R

Various R Functions from the Kostas Lab

enviGCMS

GC-MS Data Analysis for Environmental Science

enviPat

Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry

enviPick

Peak Picking for High Resolution Mass Spectrometry Data

envirem

Generation of ENVIREM Variables

EnviroStat

Statistical Analysis of Environmental Space-Time Processes

ENVISIONQuery

Retrieval from the ENVISION bioinformatics data portal into R

envlpaster

Enveloping the Aster Model

EnvNicheR

Niche Estimation

EnvStats

Package for Environmental Statistics, Including US EPA Guidance

epade

Easy Plots

epandist

Statistical Functions for the Censored and Uncensored Epanechnikov Distribution

epanetReader

Read Epanet Files into R

EPGLM

Gaussian Approximation of Bayesian Binary Regression Models

Epi

A Package for Statistical Analysis in Epidemiology

Epi

A Package for Statistical Analysis in Epidemiology

epibasix

Elementary Epidemiological Functions for Epidemiology and Biostatistics

EpiBayes

Implements Hierarchical Bayesian Models for Epidemiological Applications

EpiContactTrace

Epidemiological Tool for Contact Tracing

epidata

Tools to Retrieve Economic Policy Institute Data Library Extracts

epiDisplay

Epidemiological Data Display Package

EpiDynamics

Dynamic Models in Epidemiology

EpiEstim

EpiEstim: a package to estimate time varying reproduction numbers from epidemic curves.

epifit

Flexible Modelling Functions for Epidemiological Data Analysis

epiG

DNA methylation and SNP calling for bisulfite sequencing data

epigenomix

Epigenetic and gene transcription data normalization and integration with mixture models

EpiModel

Mathematical Modeling of Infectious Disease

epinet

Epidemic/Network-Related Tools

epinetics

EpiNetics

epineticseq

EpiNeticSeq

epiR

Tools for the Analysis of Epidemiological Data

EPISbigRR

Generalized Ridge Regression for Analysis of Interaction Effects

episensr

Basic Sensitivity Analysis of Epidemiological Results

episheet

Rothman's Episheet

episplineDensity

Density Estimation with Soft Information by Exponential Epi-splines

epistasis

Detecting Epistatic Selection with Partially Observed Genotype Data

epitools

Epidemiology Tools

EpitopePrediction

Predict Binding Between Peptides and MHC Molecules

epivizr

R Interface to epiviz web app

epivizrData

Data Management API for epiviz interactive visualization app

epivizrServer

WebSocket server infrastructure for epivizr apps and packages

epivizrStandalone

Run Epiviz Interactive Genomic Data Visualization App within R

EpiWeek

Conversion Between Epidemiological Weeks and Calendar Dates

Eplot

Plotting longitudinal series

epoc

EPoC (Endogenous Perturbation analysis of Cancer)

epr

Easy polynomial regression

EQL

Extended-Quasi-Likelihood-Function (EQL)

eqs2lavaan

EQS Output Conversion to lavaan Functions

eqtl

Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

equate

Observed-Score Linking and Equating

equateIRT

Direct, Chain and Average Equating Coefficients with Standard Errors Using IRT Methods

equivalence

Provides Tests and Graphics for Assessing Tests of Equivalence

erah

Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

erboost

Nonparametric Multiple Expectile Regression via ER-Boost

erccdashboard

Assess Differential Gene Expression Experiments with ERCC Controls

erer

Empirical Research in Economics with R

ergm

Fit, Simulate and Diagnose Exponential-Family Models for Networks

ergm.count

Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges

ergm.ego

Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data

ergm.graphlets

ERG Modeling Based on Graphlet Properties

ergmharris

Local Health Department network data set

ergm.rank

Fit, Simulate and Diagnose Exponential-Family Models for Rank-Order Relational Data

ergm.userterms

User-specified terms for the statnet suite of packages

EricksenLeslie

numerical solution of Ericsken-Leslie equations for 1D liquid crystal cells

eRm

Extended Rasch Modeling

eRm

Extended Rasch Modeling

erma

epigenomic road map adventures

ERP

Significance Analysis of Event-Related Potentials Data

erp.easy

Event-Related Potential (ERP) Data Exploration Made Easy

erpR

Event-related potentials (ERP) analysis, graphics and utility functions

erpR

Event-related potentials (ERP) analysis, graphics and utility functions

errint

Builds Error Intervals

errorizer

Function Errorizer

errorlocate

Locate Errors with Validation Rules

ES

Edge Selection

esaBcv

Estimate Number of Latent Factors and Factor Matrix for Factor Analysis

esaddle

Extended Empirical Saddlepoint Density Approximation

esc

Effect Size Computation for Meta Analysis

ESEA

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

esetVis

Visualizations of expressionSet Bioconductor object

ESG

ESG - A package for asset projection

ESGtoolkit

Toolkit for the simulation of financial assets and interest rates models.

ESKNN

Ensemble of Subset of K-Nearest Neighbours Classifiers for Classification and Class Membership Probability Estimation

ESM

Ecological Specificity Measures

esmisc

Misc Functions of Eduard SzÃ¶cs

espa.tools

Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities

estatapi

R Interface to e-Stat API

EstCRM

Calibrating Parameters for the Samejima's Continuous IRT Model

EstHer

Estimation of Heritability in High Dimensional Sparse Linear Mixed Models using Variable Selection

estimability

Tools for Assessing Estimability of Linear Predictions

estimate

Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data

estout

Estimates Output

EstSimPDMP

Estimation and Simulation for PDMPs

etable

Easy Table

etanalysis

Analysis of Eye-tracker data

ETAS

Modeling Earthquake Data Using ETAS Model

etasFLP

Mixed FLP and ML Estimation of ETAS Space-Time Point Processes

ETC

Equivalence to control

etl

Extract-Transform-Load Framework for Medium Data

ETLUtils

Utility Functions to Execute Standard Extract/Transform/Load Operations (using Package 'ff') on Large Data

etm

Empirical Transition Matrix

etma

Epistasis Test in Meta-Analysis

etrunct

Computes Moments of Univariate Truncated t Distribution

etseed

Client for 'etcd', a 'Key-value' Database

eudysbiome

Cartesian plot and contingency test on 16S Microbial data

eulerian

eulerian: A package to find eulerian paths from graphs

eulerr

Area-Proportional Euler Diagrams

euroformix

Package for intepretation of quantitative DNA mixtures

euroMix

Calculations for DNA Mixtures

euroMix

Calculations for DNA mixtures

euroMixR

Calculations for DNA mixtures, only R code

europepmc

R Interface to the Europe PubMed Central RESTful Web Service

europop

Historical Populations of European Cities, 1500-1800

EurosarcBayes

Bayesian Single Arm Sample Size Calculation Software

eurostat

Tools for Eurostat Open Data

eva

Extreme Value Analysis with Goodness-of-Fit Testing

EvalEst

Dynamic Systems Estimation - Extensions

evaluate

Parsing and Evaluation Tools that Provide More Details than the Default

EvaluationMeasures

Collection of Model Evaluation Measure Functions

Evapotranspiration

Modelling Actual, Potential and Reference Crop Evapotranspiration

evclass

Evidential Distance-Based Classification

evclust

Evidential Clustering

EvCombR

Evidence Combination in R

evd

Functions for Extreme Value Distributions

evdbayes

Bayesian Analysis in Extreme Value Theory

eVenn

A Powerful Tool to Quickly Compare Huge Lists and Draw Venn Diagrams

event

Event History Procedures and Models

eventInterval

Sequential Event Interval Analysis

events

Store and manipulate event data

events

Store and manipulate event data

eventstudies

Event study and extreme event analysis

EventTree

Event Trees for Hazard and Risk Analysis

evidenceFactors

Reporting Tools for Sensitivity Analysis of Evidence Factors in Observational Studies

evir

Extreme Values in R

evir

Extreme Values in R

evmix

Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation

evobiR

Comparative and Population Genetic Analyses

evolqg

Tools for Evolutionary Quantitative Genetics

evolvability

Calculation of Evolvability Parameters

Evomorph

Evolutionary Morphometric Simulation

evoper

Evolutionary Parameter Estimation for 'Repast Simphony' Models

EvoRAG

Evolutionary Rates Across Gradients

evt0

Mean of order p, peaks over random threshold Hill and high quantile estimates

evtree

Evolutionary Learning of Globally Optimal Trees

evtree

Evolutionary Learning of Globally Optimal Trees

EW

Edgeworth Expansion

ewc

Edge-Weighted Closeness

EWCE

Expression Weighted Celltype Enrichment

EWGoF

Goodness-of-Fit Tests for the Exponential and Two-Parameter Weibull Distributions

Exact

Unconditional Exact Test

exact2x2

Exact Conditional Tests and Confidence Intervals for 2x2 tables

exactci

Exact P-Values and Matching Confidence Intervals for Simple Discrete Parametric Cases

ExactCIdiff

Inductive Confidence Intervals for the difference between two proportions

exactLoglinTest

Monte Carlo Exact Tests for Log-linear models

exactmeta

Exact fixed effect meta analysis

ExactPath

Exact solution paths for regularized LASSO regressions with L_1 penalty

exactRankTests

Exact Distributions for Rank and Permutation Tests

ExactSampling

ExactSampling: risk evaluation using exact resampling methods for the k Nearest Neighbor algorithm.

exams

Automatic Generation of Exams in R

exams

Automatic Generation of Exams in R

ExceedanceTools

Confidence regions for exceedance sets and contour lines

excel.link

Convenient Data Exchange with Microsoft Excel

exCon

Interactive Exploration of Contour Data

excursions

Excursion Sets and Contour Credibility Regions for Random Fields

exec

Execute scripts in exec directory of packages

exif

Read EXIF Metadata from JPEGs

exifr

EXIF Image Data in R

ExiMiR

R functions for the normalization of Exiqon miRNA array data

ExLiebeRes

Exact Liebermann/Reshnikov and Bruhn-Suhr/Krumbholz plans

exomeCopy

Copy number variant detection from exome sequencing read depth

ExomeDepth

Calls Copy Number Variants from Targeted Sequence Data

exomePeak

exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis

exp2flux

Convert Gene EXPression Data to FBA FLUXes

expandFunctions

Feature Matrix Builder

expands

Expanding Ploidy and Allele-Frequency on Nested Subpopulations

ExpDE

Modular Differential Evolution for Experimenting with Operators

ExpDes

Experimental Designs package

ExpDes.pt

Pacote Experimental Designs (Portuguese)

ExpectedReturns

Computation of implied expected returns

expectile

Modelling of expectiles

expectreg

Expectile and Quantile Regression

experiment

experiment: R package for designing and analyzing randomized experiments

ExperimentHub

Client to access ExperimentHub resources

ExperimentHubData

Add resources to ExperimentHub

expert

Modeling without data using expert opinion

expint

Exponential Integral and Incomplete Gamma Function

ExplainPrediction

Explanation of Predictions for Classification and Regression Models

explor

Interactive Interfaces for Results Exploration

explorase

GUI for exploratory data analysis of systems biology data

exploreR

Tools for Quickly Exploring Data

expm

Matrix Exponential

expoRkit

Expokit in R

ExPosition

Exploratory analysis with the singular value decomposition.

expoTree

Calculate density dependent likelihood of a phylogenetic tree

expp

Spatial analysis of extra-pair paternity

ExpressionAtlas

Download datasets from EMBL-EBI Expression Atlas

ExpressionView

Visualize biclusters identified in gene expression data

exprso

Rapid Implementation of Machine Learning Algorithms for Genomic Data

expsmooth

Data Sets from "Forecasting with Exponential Smoothing"

expss

Some Useful Functions from Spreadsheets and 'SPSS' Statistics

exptest

Tests for Exponentiality

exreport

Fast, Reliable and Elegant Reproducible Research

EXRQ

Extreme Regression of Quantiles

exsic

Convenience Functions for Botanists to Create Specimens Indices

ExtDist

Extending the Range of Functions for Probability Distributions

extendedForest

Breiman and Cutler's random forests for classification and regression

exteriorMatch

Constructs the Exterior Match from Two Matched Control Groups

extfunnel

Additional Funnel Plot Augmentations

extlasso

Maximum penalized likelihood estimation with extended lasso penalty

extraBinomial

Extra-binomial approach for pooled sequencing data

extracat

Categorical Data Analysis and Visualization

extraDistr

Additional Univariate and Multivariate Distributions

extrafont

Tools for using fonts

extrafontdb

Package for holding the database for the extrafont package

extraTrees

Extremely Randomized Trees (ExtraTrees) Method for Classification and Regression

ExtremalDep

Extremal Dependence Models

ExtremeBounds

Extreme Bounds Analysis (EBA)

extremefit

Estimation of Extreme Conditional Quantiles and Probabilities

extRemes

Extreme Value Analysis

extremeStat

Extreme Value Statistics and Quantile Estimation

extremevalues

Univariate Outlier Detection

extremogram

Estimation of Extreme Value Dependence for Time Series Data

extWeibQuant

Estimate Lower Extreme Quantile with the Censored Weibull MLE and Censored Weibull Mixture

eyelinker

Load Raw Data from Eyelink Eye Trackers

eyetracking

Eyetracking Helper Functions

eyetrackingR

Eye-Tracking Data Analysis

ez

Easy Analysis and Visualization of Factorial Experiments

EZ2

Modeling Human Response Times and Accuracy using the EZ/EZ2 Diffusion Model

ezec

Easy Interface to Effective Concentration Calculations

ezglm

selects significant non-additive interaction between two variables using fast GLM implementation.

ezknitr

Avoid the Typical Working Directory Pain When Using 'knitr'

ezsim

provide an easy to use framework to conduct simulation

ezsummary

Generate Data Summary in a Tidy Format

fabCI

FAB Confidence Intervals

fabia

FABIA: Factor Analysis for Bicluster Acquisition

fACD

Autoregressive Conditional Duration Models in R

face

Fast Covariance Estimation for Sparse Functional Data

facopy

Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

FacPad

Bayesian Sparse Factor Analysis model for the inference of pathways responsive to drug treatment

factDesign

Factorial designed microarray experiment analysis

FactMixtAnalysis

Factor Mixture Analysis with covariates

FACTMLE

Maximum Likelihood Factor Analysis

FactoClass

Combination of Factorial Methods and Cluster Analysis

factoextra

Extract and Visualize the Results of Multivariate Data Analyses

FactoMineR

Multivariate Exploratory Data Analysis and Data Mining

factorAnalytics

Factor Analytics

FactorAnalytics

Functions for performing factor analysis on financial time series

factorcpt

Simultaneous Change-Point and Factor Analysis

FactoRizationMachines

Machine Learning with Higher-Order Factorization Machines

factorplot

Graphical Presentation of Simple Contrasts

factorplot

factorplot

factorQR

Bayesian quantile regression factor models

factorstochvol

Bayesian Estimation of (Sparse) Latent Factor Stochastic Volatility Models

Factoshiny

Perform Factorial Analysis from 'FactoMineR' with a Shiny Application

FACTscorer

Scores the FACT and FACIT Family of Patient-Reported Outcome Measures

factualR

thin wrapper for the Factual.com server API

FADA

Variable Selection for Supervised Classification in High Dimension

FAdist

Distributions that are Sometimes Used in Hydrology

Fahrmeir

Data from the Book "Multivariate Statistical Modelling Based on Generalized Linear Models", First Edition, by Ludwig Fahrmeir and Gerhard Tutz

fail

File Abstraction Interface Layer (FAIL)

FAiR

Factor Analysis in R

faisalconjoint

Faisal Conjoint Model: A New Approach to Conjoint Analysis

fakeplace

Generate fake geographies

fakeR

Simulates Data from a Data Frame of Different Variable Types

falcon

Finding Allele-Specific Copy Number in Next-Generation Sequencing Data

falconx

Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data

FamAgg

Pedigree Analysis and Familial Aggregation

fame

Interface for FAME Time Series Database

FamEvent

Family Age-at-Onset Data Simulation and Penetrance Estimation

Familias

Probabilities for Pedigrees Given DNA Data

FAMILY

A Convex Formulation for Modeling Interactions with Strong Heredity

FAmle

Maximum Likelihood and Bayesian Estimation of Univariate Probability Distributions

FAMT

Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data

fanc

Penalized Likelihood Factor Analysis via Nonconvex Penalty

fANCOVA

Nonparametric Analysis of Covariance

fancycut

A Fancy Version of 'base::cut'

fanovaGraph

Building Kriging Models from FANOVA Graphs

fanplot

Visualisation of Sequential Probability Distributions Using Fan Charts

FAOSTAT

Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations

faoutlier

Influential Case Detection Methods for Factor Analysis and Structural Equation Models

far

Modelization for Functional AutoRegressive Processes

faraway

Functions and Datasets for Books by Julian Faraway

farff

A Faster 'ARFF' File Reader and Writer

fArma

ARMA Time Series Modelling

fArma

Rmetrics - Modelling ARMA Time Series Processes

farms

FARMS - Factor Analysis for Robust Microarray Summarization

farsi

Translate integers into persian

fAsianOptions

EBM and Asian Option Valuation

fAsianOptions

Rmetrics - EBM and Asian Option Valuation

fAssets

Rmetrics - Analysing and Modelling Financial Assets

fAssets

Rmetrics - Analysing and Modelling Financial Assets

fassoc

VARIANCE COMPONENT BASED MULTI-MARKER ASSOCIATION TEST USING FAMILY AND UNRELATED DATA

fast

Implementation of the Fourier Amplitude Sensitivity Test (FAST)

fastAdaboost

a Fast Implementation of Adaboost

FastBandChol

Fast Estimation of a Covariance Matrix by Banding the Cholesky Factor

fastclime

A Fast Solver for Parameterized LP Problems, Constrained L1 Minimization Approach to Sparse Precision Matrix Estimation and Dantzig Selector

fastcluster

Fast Hierarchical Clustering Routines for R and Python

fastcmh

Significant Interval Discovery with Categorical Covariates

fastcox

Lasso and elastic-net penalized Cox's regression in high dimensions models using the cocktail algorithm

fastdigest

Fast, Low Memory-Footprint Digests of R Objects

fasteraster

Raster Image Processing and Vector Recognition

fastGHQuad

Fast Rcpp implementation of Gauss-Hermite quadrature

FastGP

Efficiently Using Gaussian Processes with Rcpp and RcppEigen

fastGraph

Fast Drawing and Shading of Graphs of Statistical Distributions

FastHCS

Robust Algorithm for Principal Component Analysis

fastHICA

Hierarchical Independent Component Analysis: a Multi-Scale Sparse Non-Orthogonal Data-Driven Basis

fastHorseshoe

The Elliptical Slice Sampler for Bayesian Horseshoe Regression

fastICA

FastICA Algorithms to perform ICA and Projection Pursuit

FastImputation

Learn from Training Data then Quickly Fill in Missing Data

FastKM

A Fast Multiple-Kernel Method Based on a Low-Rank Approximation

FastKNN

Fast k-Nearest Neighbors

fastLiquidAssociation

functions for genome-wide application of Liquid Association

fastLSU

Fast Linear Step Up Procedure of Benjaminiâ€“Hochberg FDR Method for Huge-Scale Testing Problems

fastM

Fast Computation of Multivariate M-estimators

fastmatch

Fast match() function

fastnet

Large-Scale Social Network Analysis

FastPCS

FastPCS Robust Fit of Multivariate Location and Scatter

fastpseudo

Fast Pseudo Observations

fastR

Foundations and Applications of Statistics Using R

fastR

Data sets and utilities for Foundations and Applications of Statistics by R Pruim

FastRCS

Fits the FastRCS Robust Multivariable Linear Regression Model

FastRWeb

Fast Interactive Framework for Web Scripting Using R

fastseg

fastseg - a fast segmentation algorithm

fastSOM

Fast Calculation of Spillover Measures

fasttime

Fast Utility Function for Time Parsing and Conversion

fat2Lpoly

Two-Locus Family-Based Association Test with Polytomic Outcome

FatTailsR

Kiener Distributions and Fat Tails in Finance

FaultTree

Fault Trees for Risk and Reliability Analysis

FaultTree.SCRAM

Interaction between FaultTree on R and SCRAM

fauxpas

HTTP Error Helpers

favnums

A Dataset of Favourite Numbers

FAwR

Functions and Datasets for "Forest Analytics with R"

fbar

An Extensible Approach to Flux Balance Analysis

fBasics

Rmetrics - Markets and Basic Statistics

fBasics

Rmetrics - Markets and Basic Statistics

fbati

Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families

FBFsearch

Algorithm for Searching the Space of Gaussian Directed Acyclic Graph Models Through Moment Fractional Bayes Factors

FBN

FISH Based Normalization and Copy Number inference of SNP microarray data

fBonds

Bonds and Interest Rate Models

fBonds

Rmetrics - Pricing and Evaluating Bonds

fbRads

Analyzing and Managing Facebook Ads from R

fbRanks

Association Football (Soccer) Ranking via Poisson Regression

fbroc

Fast Algorithms to Bootstrap Receiver Operating Characteristics Curves

fCCAC

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

fcd

Fused Community Detection

fCertificates

Basics of Certificates and Structured Products Valuation

fCertificates

fCertificates - Basics of Certificates and Structured Products Valuation

FCGR

Fatigue Crack Growth in Reliability

fCI

f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

fclust

Fuzzy Clustering

FCMapper

Fuzzy Cognitive Mapping

FCNN4R

Fast Compressed Neural Networks for R

fCopulae

Rmetrics - Bivariate Dependence Structures with Copulae

fCopulae

Rmetrics - Bivariate Dependence Structures with Copulae

fcros

A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

FD

Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology

FD

Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology

fda

Functional Data Analysis

fda

Functional Data Analysis

fdakma

Functional Data Analysis: K-Mean Alignment

fdaMixed

Functional data analysis in a mixed model framework

fdapace

Functional Data Analysis and Empirical Dynamics

fdaPDE

Functional Data Analysis and Partial Differential Equations; Statistical Analysis of Functional and Spatial Data, Based on Regression with Partial Differential Regularizations

fdasrvf

Elastic Functional Data Analysis

fdatest

Interval Testing Procedure for Functional Data

fda.usc

Functional Data Analysis and Utilities for Statistical Computing

FDboost

Boosting Functional Regression Models

FDboost

Boosting Functional Regression Models

fdcov

Analysis of Covariance Operators

FDGcopulas

Multivariate Dependence with FDG Copulas

fdnonpar

Methods for Multivariate or Functional Data

fdq

Forest Data Quality

fdrame

FDR adjustments of Microarray Experiments (FDR-AME)

fdrci

Permutation-Based FDR Point and Confidence Interval Estimation

fdrDiscreteNull

False Discovery Rate Procedure Under Discrete Null Distributions

FDRreg

False discovery rate regression

FDRsampsize

Compute Sample Size that Meets Requirements for Average Power and FDR

fdrtool

Estimation of (Local) False Discovery Rates and Higher Criticism

fds

Functional data sets

fdth

Frequency Distribution Tables, Histograms and Polygons

FeaLect

Scores Features for Feature Selection

feather

R Bindings to the Feather 'API'

feature

Local Inferential Feature Significance for Multivariate Kernel Density Estimation

FeatureHashing

Creates a Model Matrix via Feature Hashing with a Formula Interface

features

Feature Extraction for Discretely-Sampled Functional Data

fechner

Fechnerian Scaling of Discrete Object Sets

fEcofin

Economic and Financial Data Sets

fecR

Fishing Effort Calculator in R

FedData

Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources

federalregister

Client Package for the U.S. Federal Register API

FeedbackTS

Analysis of Feedback in Time Series

feedeR

Read RSS/Atom Feeds from R

FEM

Identification of Functional Epigenetic Modules

FENmlm

Fixed Effects Nonlinear Maximum Likelihood Models

fermicatsR

Fermi Large Area Telescope Catalogs

fExoticOptions

Exotic Option Valuation

fExoticOptions

Rmetrics - Pricing and Evaluating Exotic Option

fExpressCertificates

fExpressCertificates - Structured Products Valuation for ExpressCertificates/Autocallables

fExpressCertificates

fExpressCertificates - Structured Products Valuation for ExpressCertificates/Autocallables

fExtremes

Rmetrics - Modelling Extreme Events in Finance

fExtremes

Rmetrics - Extreme Financial Market Data

ff

memory-efficient storage of large data on disk and fast access functions

ffbase

Basic Statistical Functions for Package 'ff'

FFD

Freedom from Disease

FFD

Freedom from Disease

FField

Force field simulation for a set of points

ffmanova

Fifty-fifty MANOVA

ffpe

Quality assessment and control for FFPE microarray expression data

ffstream

Forgetting Factor Methods for Change Detection in Streaming Data

fftrees

Fast- and Frugal Tree Analysis

FFTrees

Generate, Visualise, and Compare Fast and Frugal Decision Trees

fftw

Fast FFT and DCT based on FFTW

fftwtools

Wrapper for FFTW3: Includes 1-D, Univariate and Multivariate, and 2-D Transform

fgac

Generalized Archimedean Copula

FGalgorithm

Flury and Gautschi algorithms

fGarch

Rmetrics - Autoregressive Conditional Heteroskedastic Modelling

fGarch

Rmetrics - Modelling Autoregressive Conditional Heteroskedasticity

FGM

Floating Grid Method

Fgmutils

Forest Growth Model Utilities

FGN

Fractional Gaussian Noise and power law decay time series model fitting

FGNet

Functional Gene Networks derived from biological enrichment analyses

fgof

Fast Goodness-of-fit Test

fgpt

Floating Grid Permutation Technique

fgpt

Floating Grid Permutation Technique

fgsea

Fast Gene Set Enrichment Analysis

FGSG

Feature Grouping and Selection Over an Undirected Graph

fgui

Function GUI

fheatmap

Fantastic Heatmap

FHtest

Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class

FI

Provide functions for forest inventory calculations

FIACH

Retrospective Noise Control for fMRI

fICA

Classical, Reloaded and Adaptive FastICA Algorithms

fields

Tools for Spatial Data

FieldSim

Random Fields (and Bridges) Simulations

fiery

A Lightweight and Flexible Web Framework

fifer

A collection of miscellaneous functions.

fiftystater

Map Data to Visualize the Fifty U.S. States with Alaska and Hawaii Insets

filehash

Simple Key-Value Database

filehashSQLite

Simple key-value database using SQLite

filematrix

File-Backed Matrix Class with Convenient Read and Write Access

filenamer

Easy Management of File Names

files

Effective File Navigation from the R Console

fImport

Rmetrics - Importing Economic and Financial Data

fImport

Rmetrics - Economic and Financial Data Import

FinAna

Financial Analysis and Regression Diagnostic Analysis

financial

Solving financial problems in R

FinancialInstrument

Financial Instrument Model Infrastructure for R

FinancialInstrument

Financial Instrument Model Infrastructure for R

FinancialMath

Financial Mathematics for Actuaries

FinAsym

Classifies implicit trading activity from market quotes and computes the probability of informed trading

FinCal

Time Value of Money, Time Series Analysis and Computational Finance

finch

Parse Darwin Core Files

fincov

Methods for estimating covariance matrices

FinCovRegularization

Covariance Matrix Estimation and Regularization for Finance

FindAllRoots

Find all root(s) of the equation and Find root(s) of the equation by dichotomy

FindIt

Finding Heterogeneous Treatment Effects

FindMinIC

Find Models with Minimum IC

FindMyFriends

Microbial Comparative Genomics in R

findpython

Python tools to find an acceptable python binary

findviews

A View Generator for Multidimensional Data

FinePop

Fine-Scale Population Analysis

fingerprint

Functions for Processing Binary Fingerprint Data

fingerprint

Functions to operate on binary fingerprint data

finiteruinprob

Computation of the Probability of Ruin Within a Finite Time Horizon

finreportr

Financial Data from U.S. Securities and Exchange Commission

FinTS

Companion to Tsay (2005) Analysis of Financial Time Series

FinTS

Companion to Tsay (2005) Analysis of Financial Time Series

FIRMAGene

FIRMAGene - differential splicing for Affymetrix Gene 1.0 ST

FISHalyseR

FISHalyseR a package for automated FISH quantification

FisherEM

The Fisher-EM algorithm

fisheyeR

Fisheye and Hyperbolic-space-alike Interactive Visualization Tools in R

fisheyeR

Fisheye and Hyperbolic-space-alike Interactive Visualization Tools in R

FisHiCal

Iterative FISH-based Calibration of Hi-C Data

fishkirkko2015

Dataset of Measurements of Fish Species at Kirkkojarvi Lake, Finland

fishkirkko2015

Dataset of Measurements of Fish Species at Kirkkojarvi Lake, Finland

fishmethods

Fishery Science Methods and Models in R

fishMod

Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models

fishmove

Prediction of Fish Movement Parameters

FIT

Transcriptomic Dynamics Models in Field Conditions

fit4NM

NONMEM platform

FitAR

Subset AR Model Fitting

FitARMA

FitARMA: Fit ARMA or ARIMA using fast MLE algorithm

fitbitScraper

Scrapes Data from Fitbit

fitcoach

Personalized Coach for Fitbit and R API

fitdc

Garmin FIT File Decoder

fitdistrplus

Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

fitdistrplus

Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

fitDRC

Fitting Density Ratio Classes

FitHiC

Confidence estimation for intra-chromosomal contact maps

fitmixst4

Fitting mixture of skew t distribution

fit.models

fit.models

fit.models

fit.models

fitob

General solvers for the general Black-Scholes (Fokker Planck) partial differential equation (PDE) in a multi-dimensional setting with main application in finance (option pricing).

fitplc

Fit Hydraulic Vulnerability Curves

FITSio

FITS (Flexible Image Transport System) Utilities

fitTetra

fitTetra is an R package for assigning tetraploid genotype scores

fivethirtyeight

Data and Code Behind the Stories and Interactives at 'FiveThirtyEight'

fixedTimeEvents

The Distribution of Distances Between Discrete Events in Fixed Time

FixSeqMTP

Fixed Sequence Multiple Testing Procedures

fizzbuzzR

Fizz Buzz Implementation

FKF

Fast Kalman Filter

FKF

Fast Kalman Filter

flacco

Feature-Based Landscape Analysis of Continuous and Constraint Optimization Problems

flagme

Analysis of Metabolomics GC/MS Data

flam

Fits Piecewise Constant Models with Data-Adaptive Knots

flan

FLuctuation ANalysis on Mutation Models

flare

Family of Lasso Regression

flars

Functional LARS

flashClust

Implementation of optimal hierarchical clustering

FLAssess

Generic classes and methods for stock assessment models

FLBEIA

Bio-Economic Impact Assessment of Management strategies using FLR

FLCore

Core package of FLR, fisheries modelling in R.

FLEDA

Exploratory Data Analysis for FLR

FLExamples

Example datasets for FLR manuals and tutorials

FlexBayes

Flexible Bayesian Inference

flexclust

Flexible Cluster Algorithms

flexCWM

Flexible Cluster-Weighted Modeling

flexdashboard

R Markdown Format for Flexible Dashboards

flexmix

Flexible Mixture Modeling

FlexParamCurve

Tools to Fit Flexible Parametric Curves

flexPM

Flexible Parametric Models for Censored and Truncated Data

flexrsurv

Flexible Relative Survival

flexsurv

Flexible Parametric Survival and Multi-State Models

flexsurv

Flexible parametric survival models

flifo

Don't Get Stuck with Stacks in R

flightcallr

Classify Night Flight Calls Based on Acoustic Measurements

FLightR

Hidden Markov Model for Solar Geolocation Archival Tags

FLIM

Farewellâ€™s Linear Increments Model

flip

Multivariate Permutation Tests

flipflop

Fast lasso-based isoform prediction as a flow problem

flippant

Dithionite Scramblase Assay Analysis

FLLat

Fused Lasso Latent Feature Model

flock

Process Synchronization Using File Locks

flock

Process Synchronization Using File Locks

flora

Tools for Interacting with the Brazilian Flora 2020

flowAI

Automatic and interactive quality control for flow cytometry data

flowBeads

flowBeads: Analysis of flow bead data

flowBin

Combining multitube flow cytometry data by binning

flowcatchR

Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

flowCHIC

Analyze flow cytometric data using histogram information

flowCL

Semantic labelling of flow cytometric cell populations

flowClean

flowClean

flowClust

Clustering for Flow Cytometry

flowCore

flowCore: Basic structures for flow cytometry data

flowCyBar

Analyze flow cytometric data using gate information

flowDensity

Sequential Flow Cytometry Data Gating

flowDiv

Cytometric Diversity Indices from 'FlowJo' Workspaces

flower

Tools for characterizing flowering traits

flowfield

Forecasts future values of a univariate time series.

flowFit

Estimate proliferation in cell-tracking dye studies

flowFlowJo

Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.

flowFP

Fingerprinting for Flow Cytometry

flowMap

Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test

flowMatch

Matching and meta-clustering in flow cytometry

flowMeans

Non-parametric Flow Cytometry Data Gating

flowMerge

Cluster Merging for Flow Cytometry Data

flowPeaks

An R package for flow data clustering

flowPhyto

Methods for Continuous Flow Cytometry

flowPloidy

Analyze flow cytometer data to determine sample ploidy

flowPlots

flowPlots: analysis plots and data class for gated flow cytometry data

flowQ

Quality control for flow cytometry

flowQB

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

flowr

Streamlining Design and Deployment of Complex Workflows

FlowRepositoryR

FlowRepository R Interface

flows

Flow Selection and Analysis

FlowScreen

Daily Streamflow Trend and Change Point Screening

FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data

flowStats

Statistical methods for the analysis of flow cytometry data

flowTrans

Parameter Optimization for Flow Cytometry Data Transformation

flowType

Phenotyping Flow Cytometry Assays

flowUtils

Utilities for flow cytometry

flowViz

Visualization for flow cytometry

flowVS

Variance stabilization in flow cytometry (and microarrays)

flowWorkspace

Infrastructure for representing and interacting with the gated cytometry

FLR

Fuzzy Logic Rule Classifier

flsa

Path algorithm for the general Fused Lasso Signal Approximator

FLSSS

Multi-Threaded Multidimensional Fixed Size Subset Sum Solver and Extension to General-Purpose Knapsack Problem

Flury

Data Sets from Flury, 1997

flux

Flux rate calculation from dynamic closed chamber measurements

FLXSA

eXtended Survivor Analysis for FLR

fma

Data Sets from "Forecasting: Methods and Applications" by Makridakis, Wheelwright & Hyndman (1998)

fMarkovSwitching

R Package for Estimation, Simulation and Forecasting of a Univariate Markov Switching Model

fmcsR

Mismatch Tolerant Maximum Common Substructure Searching

fmdates

Financial Market Date Calculations

FME

A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis

FME

A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis

FMP

Filtered Monotonic Polynomial IRT Models

fmri

Analysis of fMRI Experiments

fmrs

Variable Selection in Finite Mixture of AFT Regression and FMR

fmsb

Functions for Medical Statistics Book with some Demographic Data

FMsmsnReg

Regression Models with Finite Mixtures of Skew Heavy-Tailed Errors

FMStable

Finite Moment Stable Distributions

fmt

Variance estimation of FMT method (Fully Moderated t-statistic)

fMultivar

Rmetrics - Analysing and Modeling Multivariate Financial Return Distributions

fMultivar

Rmetrics - Analysing and Modeling Multivariate Financial Return Distributions

FNN

Fast Nearest Neighbor Search Algorithms and Applications

fNonlinear

Rmetrics - Nonlinear and Chaotic Time Series Modelling

fNonlinear

Nonlinear and Chaotic Time Series Modelling

foba

greedy variable selection

focalCall

Detection of focal aberrations in DNA copy number data

fontBitstreamVera

Fonts with Bitstream Vera Fonts Licence

fontcm

Computer Modern font for use with extrafont package

fontLiberation

Liberation Fonts

fontquiver

Set of Installed Fonts

foodweb

visualisation and analysis of food web networks

foodweb

Generating food webs

fOptions

Rmetrics - Pricing and Evaluating Basic Options

fOptions

Rmetrics - Pricing and Evaluating Basic Options

ForAI

Forecasting with Artificial Intelligence

forams

Foraminifera and Community Ecology Analyses

forcats

Tools for Working with Categorical Variables (Factors)

foreach

Provides Foreach Looping Construct for R

foreach

Provides Foreach Looping Construct for R

ForeCA

Forecastable Component Analysis

forecast

Forecasting Functions for Time Series and Linear Models

ForecastCombinations

Forecast Combinations

forecastHybrid

Convenient Functions for Ensemble Time Series Forecasts

forecastSNSTS

Forecasting for Stationary and Non-Stationary Time Series

forecTheta

Forecasting Time Series by Theta Models

forega

Floating-Point Genetic Algorithms with Statistical Forecast Based Inheritance Operator

foreign

Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ...

forensic

Statistical Methods in Forensic Genetics

ForensicDocument

Quantification and evaluation tools for forensic document examiners

forensim

Statistical tools for the interpretation of forensic DNA mixtures

forensim

Statistical tools for the interpretation of forensic DNA mixtures

forestFloor

Visualizes Random Forests with Feature Contributions

forestFloor

Visualizes Random Forests with Feature Contributions

forestFloorStable

(Legacy version 1.5)Visualizes Random Forests with Feature Contributions

forestinventory

Design-Based Global and Small-Area Estimations for Multiphase Forest Inventories

forestmodel

Forest Plots from Regression Models

forestplot

Advanced Forest Plot Using 'grid' Graphics

ForestTools

Analysing Remotely Sensed Forest Data

ForImp

Imputation of Missing Values Through a Forward Imputation Algorithm

ForIT

Functions from the 2nd Italian Forest Inventory (INFC)

FormalSeries

Elementary arithemtic in formal series rings

formatR

Format R Code Automatically

formattable

Create 'Formattable' Data Structures

Formula

Extended Model Formulas

Formula

Extended Model Formulas

formula.tools

Utilities for Formulas, Expressions, Calls and Other Objects

formulr

Miscelaneous tools to handle formulas.

fortunes

R Fortunes

fortunes

R Fortunes

forward

Forward search

ForwardSearch

Forward Search using asymptotic theory

fossil

Palaeoecological and Palaeogeographical Analysis Tools

FourCSeq

Package analyse 4C sequencing data

fourierin

Computes Numeric Fourier Integrals

fourPNO

Bayesian 4 Parameter Item Response Model

FourScores

FourScores - A game for two players

fpa

Spatio-Temporal Fixation Pattern Analysis

fpc

Flexible Procedures for Clustering

fpca

Restricted MLE for Functional Principal Components Analysis

FPCA2D

Two Dimensional Functional Principal Component Analysis

fpCompare

Reliable Comparison of Floating Point Numbers

FPDclustering

PD-Clustering and Factor PD-Clustering

fpop

Segmentation using Optimal Partitioning and Function Pruning

fPortfolio

Rmetrics - Portfolio Selection and Optimization

fPortfolio

Rmetrics - Portfolio Selection and Optimization

fPortfolioBacktest

Rmetrics - Portfolio Backtesting

fpow

Computing the noncentrality parameter of the noncentral F distribution

fpp

Data for "Forecasting: principles and practice"

fptdApprox

Approximation of First-Passage-Time Densities for Diffusion Processes

fracdiff

Fractionally differenced ARIMA aka ARFIMA(p,d,q) models

fracprolif

Fraction Proliferation via a Quiescent Growth Model

fractal

Fractal Time Series Modeling and Analysis

fractal

Fractal Time Series Modeling and Analysis

fractaldim