Bioconductor Packages

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

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

Basic peak calling on STARR-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

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

Bias-free Footprint Enrichment Test

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)

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

Biological Network Analysis in R

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

Detect tissue heterogeneity in expression profiles with gene sets

Write, containerize, publish and version Quarto books with Bioconductor

An interactive Shiny dashboard for Bioconductor package maintainers

Representing Different Biological Sets

Tools to aid the development of Bioconductor Workflow packages

Efficient manipulation of biological strings

This R package for performing module repertoire analyses and generating fingerprint representations

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

Code for using BridgeDb identifier mapping framework from within R

BrowserViz: interactive R/browser graphics using websockets and JSON

Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

Chromosmal Aberrations Finder in Expression data

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

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Cytometry dATa anALYSis Tools

CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks

plot bayesian network inferred from gene expression data based on enrichment analysis results

Case Control Allele Frequency Estimation

Plots For Visualising Cell-Cell Interactions

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

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

Normalization of array CGH data with imbalanced aberrations.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

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