Bioconductor Packages

Coordinate Covariation Analysis

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

Annotations for City of Hope CpG Island Analysis Pipeline

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

COexpression Tables ANalysis

CPSM: Cancer patient survival model

CRImage a package to classify cells and calculate tumour cellularity

Statistical tools for the analysis of ChIP-seq data

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

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

Data companion to CTexploreR

Explores Cancer Testis Genes

Candidate Driver Analysis

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical 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

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

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

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

ChIP-seq Target Databases for TFEA.ChIP

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

ChIPXpress Pre-built Databases

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

Chimp and human brain data package

Analysis of single-cell epigenomics datasets with a Shiny App

CiteFuse: multi-modal analysis of CITE-seq data

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

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Infers clonal composition of a tumor

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

ConsensusClusterPlus