Biocview "StatisticalMethod"

Adjust for positional and batch effects using ComBat

A Fast Scalable and Flexible Non Negative Matrix Factorization Method

A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

An algorithm to find optimal signal levels in a tree

Analysis of pooled genetic screens

Analysis of single and multiple phenomic data sets

Analyze Gene Sets Collections Properites

An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.

An R package for circadian differential R2.

An R package for DiffCircaPipeline: A framework for multifaceted characterization of differential rhythmicity

An R package for fast computing for adaptively weighted fisher's method

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

An R package for qualitative biclustering in support of gene co-expression analyses

A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

Association Plots

a statistical framework for differential pseudotime analysis in multiple single-cell RNA-seq samples

A Statistical Model for Describing and Simulating Microbial Community Profiles

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Batch Effects Correction with Unknown Subtypes

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

Bayesian Enrichment Estimation in R

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Binomial Random Forest Feature Selection

Calculate and Visualize Synergy Scores for Drug Combinations

Calculates Mulcom test

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

Classes and methods for multi-omics data integration

Clonal ordering and visualization

Clustering and Alignment of ChIP-Seq peaks based on their shapes

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

CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Comparing Differential Abundance/Expression Methods

Compensates for the bias introduced by median normalization in phosphoproteomics. This is done by taking enriched and non-enriched data and creating a normalization factor.

Concomitant identification of distinctness and similarity in gene expression analysis.

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

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

Correction of batch effects in DNA methylation data

Correlated Meta-Analysis

Correlation analysis of RNA secondary structure mutation and differential expression

Creating annotated submodules of high-throughput data through recursive partitioning

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

Decomposition of individual tumors into mutational signatures by signature refitting

Deconvolution of Expression for Nascent RNA Sequencing Data

decoupleR: Ensemble of computational methods to infer biological activities from omics data

DeMAND

Detecting hidden batch factors through data adaptive adjustment for biological effects

Detection of DE genes in time series data using impulse models

Detection of de novo deletion in targeted sequencing trios

Detect tissue heterogeneity in expression profiles with gene sets

Differential expression analysis and model fitting for single-cell RNA-seq data

Differential expression analysis of longitudinal count data sets

Differential Expression Meta-Analysis

Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

Differentially regulated genes from scRNA-seq data

Different methods for the integrative analysis multiple omics data

discussions and exercises on classical statistics for CSHL 2022

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

distinct: a method for differential analyses via hierarchical permutation tests

Divergence Computations

Divergence: Functionality for assessing omics data by divergence with respect to a baseline

Empirical Bayes estimate of block diagonal covariance matrices

Empirical Bayesian approach to mutational signature discovery

Exposome and omic data associatin and integration analysis

FABIA: Factor Analysis for Bicluster Acquisition

FEVV: Functional Enrichment of Genomic Variants and Variations

Finding differentially expressed unannotated genomic regions from RNA-seq data

Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

Flexible, isoform-level differential expression analysis

Functional similarities

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

geneChip Analysis Package

Gene expression changes in three biological conditions

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

Generate synthetic nucleosome maps

Gene Set Analysis in R

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

Gene Set Enrichment Analysis Extended to Contingency Cubes

Gene Set Enrichment Analysis with Networks

Gene Set Enrichment Meta-Analysis

genesis assocation testing code rewrite

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Genometric Correlation package

GISPA: Method for Gene Integrated Set Profile Analysis

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Handling Missing Individuals in Multi-Omics Data Integration

Hierarchical ensemble method based on factor graph

HLA Genotype Imputation with Attribute Bagging

Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Identifying differential cell populations in flow cytometry data accounting for marker frequency

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Inferring functionally related proteins using protein interaction networks

Integrated Differential Expression and Differential Network Analysis (INDEED)

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

interface to python sklearn via Rstudio reticulate

Interval-Wise Testing for Omics Data

Iteration removal method for feature selection

Iterative Clustering

Iteratively Adjusted Surrogate Variable Analysis

JODA algorithm for quantifying gene deregulation using knowledge

Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

Judging Quality of Clustering Methods using Mutual Information

Lots Of Lasso

Massive correlating biclusters for gene expression data and associated methods

Measurement Error model estimate for correlation coefficient

Mechanism-Aware Imputation

Meta-analysis of Gene Set differential Co-expression Analysis

MetaCyto: A package for meta-analysis of cytometry data

Meta Gene Set Co-expression Analysis

MethylMix: Identifying methylation driven cancer genes

Mixtures of Matrix Variate Poisson-log Normal Distributions

Mixtures of Multivariate Poisson-Log Normal Model for Clustering Count Data

'(m,n)-mer' - A Simple Statistical Feature for Sequence Classification

Model based analysis for paired-end data

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Modified Concordance Index

Molecular Signature identification using Biclustering

Multimodal Mediation Analysis

Multiomic Batch effect Correction

Multiple omics data integrative clustering and gene set analysis

Multi-sample multi-group scRNA-seq data analysis tools

Negative Binomial Models to detect Differential Splicing

Neighbor_net analysis

Network Analysis Supported by Boosting

Network-based prioritization of putative metabolite IDs

Network Centrality Metrics for Elastic-Net Regularized Models

Network-Regularized Regression Models

Online error control

Online error rate control

Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

PAIRADISE: Paired analysis of differential isoform expression

PANDA Algorithm

Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

Perform Chromosomal Ancestry Differences (CAnD) Analyses

Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

PLSDA-batch

PolyA counting and differential transcript usage analysis for scRNA-seq data

PoTRA: Pathways of Topological Rank Analysis

Predict Combined Function of Transcription Factors

Predicting Targets for Drosophila Intragenic miRNAs

Predict open reading frames in nucleotide sequences

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

Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

Profile score distributions

Quantification and Visualization of Variations of Splicing in Population

Quantification and Visulization of Variations of Splicing in Population

Quantification of the Tumor Immune contexture from RNA-seq data

Random Gene Set Enrichment Analysis

Randomization routines for Clinical Trials

Random Rotation Methods for High Dimensional Data with Batch Structure

Rank Product method for identifying differentially expressed genes with application in meta-analysis

Rcpp Integration Surrogate Variable Analysis

Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

Recovering spatially-varying cell-specific gene co-expression networks for single-cell spatial expression data.

Regression Models with Multivariate Outcomes for Mass Cytometry Experiments

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

R implementation of the LEfSE method for microbiome biomarker discovery

RNA-seq data analysis using the Poisson-Tweedie family of distributions

Robust outlier identification for DNA methylation data

Robust prediction of clinical outcomes using cytometry data without cell gating

R package for immunogenomics data handling and association analysis

rqt: utilities for gene-level meta-analysis

Rtreemix: Mutagenetic trees mixture models.

RUV for normalization of expression array data

Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

Science-wise false discovery rate and proportion of true null hypotheses estimation

Selecting the number of mutational signatures using a perplexity-based measure and cross-validation

Selecting transcript model using PRO-seq

Shiny app GUI wrapper for ggplot with built-in statistical analysis

Significance Analysis of Function and Expression

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Simulation and Deconvolution of Omic Profiles

Single Cell Differential Expression

Somatic Signatures

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Spatial point data simulator for tissue images

`SPOTlight`: Spatial Transcriptomics Deconvolution

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data

Stability and Aggregation of ranked gene lists

stageR: stage-wise analysis of high throughput gene expression data in R

Statistical Analysis of MPRA data

Statistical analysis of phenotypic data

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Subtype Identification with Survival Data

Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data

Surrogate Variable Analysis

Target Inhibition Interaction using Maximization and Minimization Averaging

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

Testing multiple biological mediators simultaneously

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

The Discordant Method: A Novel Approach for Differential Correlation

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Tools for computing, querying and storing linkage-disequilibrium data

Tools for Omics Data Analysis

Transcript abundance linear modeling from compressed coverage information

Transcription Factors Association Rules Miner

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

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

Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

Variable Selection Oriented LASSO Bagging Algorithm

Variance Adaptive Shrinkage

Visual comparison of mutational processes in a set of tumors

What the Package Does (One Line, Title Case)

XCI-inference

Yet Another Package for Signature Analysis

Biocview "StatisticalMethod"

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