Biocview "MultipleComparison"

Accurate Inference of Genetic Ancestry from Cancer Sequencing

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Adjust for positional and batch effects using ComBat

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

A graphical interface for the metagene package

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

A lecture on sequence count data

Analysis of alternative poly A site usage

Analysis of an ICA decomposition obtained on genomics data

Analysis of single-cell epigenomics datasets with a Shiny App

Analytical R tools for Mass Spectrometry

An integrated analysis package of Gene expression and Copy number alteration

an R package for analysis, visualization and biomarker discovery of microbiome

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

An R package for pathway analysis using topological information

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

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

An R package for RNA visualization and analysis

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package to detect chromatin state switches from epigenomic data

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

A package for the clinical proteomic profiling data analysis

A package to produce metagene plots

askoR - Differential Expresion Analysis using edgeR

A small RNA-seq visualizer and analysis toolkit

Assess Differential Gene Expression Experiments with ERCC Controls

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

A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data

A test for when to use quantile normalization

A toolkit for performing KNN-based statistics for flow and mass cytometry data

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

A universal enrichment tool for interpreting omics data

Automated analysis of high-throughput qPCR data

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

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

Bayesian models for differential gene expression

Benchmark of differential abundance methods on microbiome data

Big multivariate data plotted interactively

Bump Hunter

Calculates Mulcom test

Check Multiple Covariates for Potenial Confounding Effects

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

ChIP-Seq Analysis with Windows

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Clustering of high-throughput sequencing data by identifying co-expression patterns

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

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

Compare multiple ChIP-Seq experiments.

Comparison, Benchmarking & QC of Epigenomic Datasets

Condition specific detection from expression data

Confounding Explorer

Context-Aware Transcript Quantification from Long Read RNA-Seq data

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

Coordinated Gene Activity in Pattern Sets

Covariate Assisted Large-scale Multiple testing

Data-Adaptive Statistics for High-Dimensional Multiple Testing

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

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

dgeAnalysis

Differential Analyis of Hi-C Data

Differentially regulated genes from scRNA-seq data

Differential neighbourhood abundance testing on a graph

Differential Topology, Progression and Differentiation

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

DiffLogo: A comparative visualisation of biooligomer motifs

Discern RNA structure proximal to protein binding

Discriminant Analysis for Evolutionary Inference

Disease Ontology Semantic and Enrichment analysis

distinct: a method for differential analyses via hierarchical permutation tests

Empirical Analysis of Digital Gene Expression Data in R

Empirical Bayesian analysis of patterns of differential expression in count data

Empirical Method of Optimal Pvalue Weighting

Empirical RNA-seq Sample Size Analysis

Ensemble of Gene Set Enrichment Analyses

Estimating Local False Discovery Rates Using Empirical Bayes Methods

Estimating Local False Discovery Rates Using the Method of Moments

Estimation of local false discovery rate

Estimation of the false discovery rate.

Evaluation of normalization methods and calculation of differential expression analysis statistics

Exploration and Significant Biology on a Gene Set.

Exposome and omic data associatin and integration analysis

Exposome exploration and outcome data analysis

Extraction of Differential Gene Expression

FABIA: Factor Analysis for Bicluster Acquisition

FDR adjustments of Microarray Experiments (FDR-AME)

find influential TF and Target based on multi-omics data

Finding Co-occuring motifs of transcription factor binding sites

Find the most characteristic gene ontology terms for groups of human genes

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Functional Enrichment analysis

Functions to help analyze data as phyloseq objects

GaGa hierarchical model for high-throughput data analysis

Gene Environment Wide Interaction Search Threshold

Gene Expression Variation Analysis (GEVA)

Generally Applicable Gene-set Enrichment for Pathway Analysis

Generating Tree Hierarchy Visualizations from Gene Expression Data

Gene Set Analysis of (Rare) Copy Number Variants

Gene set over-representation, enrichment and network analyses for high-throughput screens

Global Test for Counts

goProfiles: an R package for the statistical analysis of functional profiles

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

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

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Handling and analysis of high-throughput microbiome census data

HLA typing clustering and visualization based on specific similarity metrics

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

Identify Moonlighting ncRNAs

ID Mapping Analysis

ID Mapping Data Retrieval

Illumina 450K methylation array spatial analysis methods

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

Independent Hypothesis Weighting

Infers clonal composition of a tumor

In-silico methods for genetic finemapping in inbred mice

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Interactive Multi-Omics Cancers Data Visualization and Analysis

Interval-Wise Testing for Omics Data

Iterative Differential Clustering for single-cell

Linear Models for Microarray Data

LinkHD: a versatile framework to explore and integrate heterogeneous data

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

Mass Cytometry S4 Class Structure Pipeline for Images

Matched Interaction across Tissues (MIxT) data analysis

MeSH Enrichment and Semantic analyses

Meta-Analyses on P-Values of Differential Analyses

Meta-analysis of high-throughput experiments using feature annotations

Meta-Analysis of High-Throughput Experiments Using Feature Annotations

Metabarcoding and microbiome analysis using multiple amplicons

Methods for identifying small RNA loci from high-throughput sequencing data

Methylated CpGs Set Enrichment Analysis

Methylation array and sequencing spatial analysis methods

Metrics to estimate a level of similarity between two ChIP-Seq profiles

Microarray Analysis of Differential Expression

Microbiome Exploration App

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Multi-Omics integration and VIsualization in Cancer Subtyping

Multiple Beta t-Tests

Multiple co-inertia analysis of omics datasets

Multiple Sequence Alignment

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Multiplex PCR Primer Design and Analysis

Multivariate analysis of microarray data using ADE4

Murine Palate miRNA Expression Analysis

Negative Binomial Beta t-Test

NGS Read Simulator for FFPE Tissue

Normalization and difference calling in ChIP-seq data

Omics Data Integration Project

Online error control

Online error rate control

Operating characteristics plus sample size and local fdr for microarray experiments

Optimal p-value weighting with independent information

OVESEG-test to detect tissue/cell-specific markers

Parametric And Resistant Outlier DYtection

Pathway Analysis

Permutation-Based Confidence for Molecular Classification

Phenotypic EMD for comparison of single-cell samples

PhyloProfile

PhyloProfileCorona

PhyloProfileRibi

Plot Gene Ontology and KEGG pathway Annotation and Abundance

Power Estimation Tool for RNA-Seq and proteomics data

Prize: an R package for prioritization estimation based on analytic hierarchy process

Produce heatmaps for RNA-Seq HIV data

PRojection Onto the Most Interesting Statistical Evidence

QC for enrichment based NGS

Quantitative comparison of multiple ChIP-seq datasets

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

RBioinf

Rcpp Integration Surrogate Variable Analysis

Reactome Pathway Analysis

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

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

Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

Resampling-based multiple hypothesis testing

Resampling Collapsed Null Distributions for Simultaneous Inference

Rhythmicity Analysis Incorporating Non-parametric Methods

R Interface with InterMine-Powered Databases

RNA-seq analysis using multiple algorithms

Robust statistical inference for quantitative LC-MS proteomics

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

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

Semi-Supervised Mixture Model

Set Based Visualizations for Next-Gen Sequencing Data

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

Similarities of Ordered Gene Lists

simple Two-Tier Mapper: an interface for Two-Tier Mapper

Single cell replicability analysis

Smooth quantile normalization

Stability Ranking

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

Statistical analysis for sparse high-throughput sequencing

Statistical Analysis of Molecular Profiles

Statistical Analysis of the GeneChip

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Statistical Tools for volume data from 2D Gel Electrophoresis

Statistics and dIagnostic Graphs for HTS

Suite of Functions for Pooled Crispr Screen QC and Analysis

Supervised Normalization of Microarrays

Surrogate Variable Analysis

T-cell Receptor/Immunoglobulin Profiler (TRIP)

Test and visualize gene overlaps

Testing multiple biological mediators simultaneously

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

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

Time-Course Multi-Omics data integration

Tool for Evaluation of Cell Identity from Transcription Profiles

Tools for manipulating GO and microarrays

Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Top Confident Effect Sizes

trajectory-based differential expression analysis for sequencing data

Turn Bioconductor objects into tidy data frames

TVTB: The VCF Tool Box

Two-Tier Mapper: a clustering tool based on topological data analysis

Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Using Mass Cytometry for Differential Abundance Analyses

Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity

Visualise microarray and RNAseq data using gene ontology annotations

Visualization of highly multiplexed imaging data in R

What the Package Does (One Line, Title Case)

Biocview "MultipleComparison"

R Package Documentation

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