Bioconductor Packages

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

Efficient manipulation of biological strings

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

Cytometry dATa anALYSis Tools

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

Case Control Allele Frequency Estimation

Co-expression Modules identification Tool

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

A normalization method for Copy Number Aberration in cancer samples

CNE Detection and Visualization

Integration of CellNOptR to add missing links

Copy Number Variant Metrics

Reliable CNV detection in targeted sequencing applications

Summarization and expression/phenotype association of CNV ranges

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Coordinate Covariation Analysis

Annotations for City of Hope CpG Island Analysis Pipeline

Data normalization by matrix raking

COexpression Tables ANalysis

Design of guide RNAs in CRISPR genome-editing systems

Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

Chip-seq Signal Quantifier Pipeline

Package for CTDbase data query, visualization and downstream analysis

Explores Cancer Testis Genes

An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

Category Analysis

This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

Causal network analysis methods

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

Reconstruction, visualization and analysis of branching trajectories

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Cepo for the identification of differentially stable genes

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

ChIP-seq Target Databases for TFEA.ChIP

ChIPXpress Pre-built Databases

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Chimp and human brain data package

Analysis of single-cell epigenomics datasets with a Shiny App

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Calculate similarity of clusters from different single cell samples using foldchanges

Coordinated Gene Activity in Pattern Sets

An Investigation Across Different Species and Tissues

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets