Bioconductor Packages

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

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

Spatial transcriptomic clustering

R SDK for BaseSpace RESTful API

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

Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data

Clustering and Resolution Enhancement of Spatial Transcriptomes

Compression of Illumina BeadArray data

Automatic RNA-Seq present/absent gene expression calls generation

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

Bias-free Footprint Enrichment Test

Processing and analyzing bisulfite sequencing data

Biclustering Analysis and Results Exploration

Binding site defintion based on iCLIP data

Functional Similarities

Bioinformatics Genetic Algorithm (BioGA)

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

BioTIP: An R package for characterization of Biological Tipping-Point

Efficient manipulation of biological strings

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

Code for using BridgeDb identifier mapping framework from within R

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

Collection of annotation related methods for mass spectrometry data

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

Case Control Allele Frequency Estimation

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

Plots For Visualising Cell-Cell Interactions

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

Statistical analysis for the Colony Formation Assay

CGHbase: Base functions and classes for arrayCGH data analysis.

Normalization of array CGH data with imbalanced aberrations.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

Fast and accurate scRNA-seq cell type identification

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

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

A normalization method for Copy Number Aberration in cancer samples

Add-on to CellNOptR: Discretized time treatments

Integration of CellNOptR to add missing links