Bioconductor Packages

Coordinate Covariation Analysis

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Data normalization by matrix raking

COexpression Tables ANalysis

CPSM: Cancer patient survival model

Design of guide RNAs in CRISPR genome-editing systems

Statistical tools for the analysis of ChIP-seq data

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

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Data companion to CTexploreR

Explores Cancer Testis Genes

Candidate Driver Analysis

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

Predict genes expressed selectively in specific cell types

Evaluate Cellspecific Mixing

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

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 Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

Analysis of single-cell epigenomics datasets with a Shiny App

CiteFuse: multi-modal analysis of CITE-seq data

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Infers clonal composition of a tumor

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Calculate similarity of clusters from different single cell samples using foldchanges

Judging Quality of Clustering Methods using Mutual Information

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

Create Copy-Number Plots using karyoploteR functionality

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

Correlation Motif Fit

Tools for counting and visualising mutations in a target location

Queries the Human Cell Atlas

Robust prediction of clinical outcomes using cytometry data without cell gating