Bioconductor Packages

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

geneChip Analysis Package

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Gene Expression Atlas query and gene set enrichment package.

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bayesian Analysis of Single-Cell Sequencing data

Stan implementation of BASiCS

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Meta-analysis for the metagenomic read counts data from different cohorts

High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

Correction of batch effects in DNA methylation data

Bayesian models for differential gene expression

BLMA: A package for bi-level meta-analysis

Refitting diploid region profiles using a clustering procedure

Model higher-order methylation profiles

Tools for the Efficient Analysis of High-Resolution Genomics Data

Software infrastructure for efficient representation of full genomes and their SNPs

Forge your own BSgenome data package

Gene network reconstruction

Batch Effects Correction with Unknown Subtypes

kallisto | bustools R utilities

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

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

Bioconductor-Friendly Multithreaded BAM Processing

R SDK for BaseSpace RESTful API

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

Single-cell RNA-seq batch effects correction methods interface

Batch Effects Quality Control Software

Identify Batch-Biased Spatially Variable Genes

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Clustering and Resolution Enhancement of Spatial Transcriptomes

Comprehensive Collection of Curated Benchmarking Datasets and their Evaluation

Coordinate-Based Genomic Visualization Package for R

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

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)

Binding site defintion based on iCLIP data

BioCarta Pathway Images

Functional Similarities

Bioinformatics Genetic Algorithm (BioGA)

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

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

Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Biological Network Analysis in R

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

Biological Network Analysis

Biobase: Base functions for Bioconductor

Read and write GFF and GTF files

Programmatic Access to the Azul API

Utility and internal functions for Bioconductor packages