Bioconductor Packages

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

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

Synthesis of microarray-based classification

Add-on to CellNOptR: Discretized time treatments

ODE add-on to CellNOptR

Reliable CNV detection in targeted sequencing applications

Coordinate Covariation Analysis

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

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

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

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

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

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

ConsensusClusterPlus

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

An R package for colorectal cancer screening and microbiome analysis

Queries the Human Cell Atlas

Power analysis for CyTOF experiments

Robust prediction of clinical outcomes using cytometry data without cell gating

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Low Dimensions projection of cytometry samples

Denoising Algorithm based on Relevance network Topology

Tools for curating, analyzing, and manipulating biological sequences

Two-sample tests on a graph

Differential gene expression analysis based on the negative binomial distribution

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Differential Expression Meta-Analysis