Bioconductor Packages

Algorithms for Calculating Microarray Enrichment (ACME)

Analysis of Microbiome Differential Abundance by Pooling Tobit Models

Microbiome differential abudance and correlation analyses with bias correction

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Bayesian Analysis of Single-Cell Sequencing data

Stan implementation of BASiCS

Refitting diploid region profiles using a clustering procedure

Batch Effects Quality Control Software

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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

A normalization method for Copy Number Aberration in cancer samples

Reliable CNV detection in targeted sequencing applications

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

Data normalization by matrix raking

CPSM: Cancer patient survival model

Chip-seq Signal Quantifier Pipeline

A mass spectrometry imaging toolbox for statistical analysis

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Analysis of single-cell epigenomics datasets with a Shiny App

An R package for colorectal cancer screening and microbiome analysis

Queries the Human Cell Atlas

Tools for the Differential Analysis of Proteins Abundance with R

Differential Composition Analysis Transformed by a Similarity matrix

Differential gene expression analysis based on the negative binomial distribution

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

DegNorm: degradation normalization for RNA-seq data

Differential Binding Analysis of ChIP-Seq Peak Data

Normalization of Single-Cell mRNA Sequencing Data

A DownStream Chemo-Proteomics Analysis Pipeline

Estimating Absolute Abundance from Microbial Spike-in Controls

An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

Quality control and analysis tools for Illumina DNA methylation BeadChip

Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Count model based differential expression and normalization on GeoMx RNA data

NanoString GeoMx Tools

R Package for Processing High Content Screening data

Filter replicated high-throughput transcriptome sequencing data

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

Hi-C Direct Caller Plus

A/B compartment detection and differential analysis

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Set of 3D genomic interaction analysis tools

Intron-Exon Retention Estimator

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Linear model and normality based normalization and transformation method (Linnorm)

Fast treatment of MACSQuantify FACS data

CGH Micro-Array NORmalization

Evaluation and correction of batch effects in microbiome data-sets

Mean/Median-balanced quantile normalization