Bioconductor Packages

COexpression Tables ANalysis

CPSM: Cancer patient survival model

Design of guide RNAs in CRISPR genome-editing systems

CRImage a package to classify cells and calculate tumour cellularity

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

Explores Cancer Testis Genes

Candidate Driver Analysis

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

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical analysis

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

Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis

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

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

Analysis of single-cell epigenomics datasets with a Shiny App

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Infers clonal composition of a tumor

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Clustering of MS2 Spectra for Metabolite Identification

ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Clustering of Immune Receptor Repertoires

Calculate similarity of clusters from different single cell samples using foldchanges

Judging Quality of Clustering Methods using Mutual Information

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

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

ConsensusClusterPlus

Create Copy-Number Plots using karyoploteR functionality

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

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Correlation Motif Fit

An R package for colorectal cancer screening and microbiome analysis

Tools for counting and visualising mutations in a target location

Queries the Human Cell Atlas

Power analysis for CyTOF experiments

Robust prediction of clinical outcomes using cytometry data without cell gating