Bioconductor Packages

R package associated to BREW3R

Software infrastructure for efficient representation of full genomes and their SNPs

Forge your own BSgenome data package

Computational pipeline for computing probability of modification from structure probing experiment data

Batch Effects Correction with Unknown Subtypes

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

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

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

Basic peak calling on STARR-seq data

Batch Effects Quality Control Software

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Clustering and Resolution Enhancement of Spatial Transcriptomes

Analysing Illumina BeadArray expression data using Bioconductor

Illumina EPIC data on BeadSorted child saliva cells

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

Bias-free Footprint Enrichment Test

Biclustering Analysis and Results Exploration

Binding site defintion based on iCLIP data

Functional Similarities

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

R-side access to BioPlex protein-protein interaction data

Detect tissue heterogeneity in expression profiles with gene sets

Nearest Neighbor Detection for Bioconductor Packages

Singular Value Decomposition for Bioconductor Packages

interface to python sklearn via Rstudio reticulate

Efficient manipulation of biological strings

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

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

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

Carbon Tetrachloride (CCl4) treated hepatocytes

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

Hub package for the precomputed data of CENTRE and example data

Statistical analysis for the Colony Formation Assay

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

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