Bioconductor Packages

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

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Cepo for the identification of differentially stable genes

ChIC package data

ChIP-seq Target Databases for TFEA.ChIP

ChIPXpress Pre-built Databases

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

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

Infers clonal composition of a tumor

Clonality testing

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

Batch Correction for DNA Methylation Data

ConsensusClusterPlus

Helper files for CopywriteR

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

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

An R package for colorectal cancer screening and microbiome analysis

An Interactive Consensus Clustering Framework for Multi-platform Data 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

A Toolkit for Flow And Mass Cytometry Data

Discriminant Analysis

Denoising Algorithm based on Relevance network Topology

Detecting hidden batch factors through data adaptive adjustment for biological effects

Tools for curating, analyzing, and manipulating biological sequences

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

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

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated CpG using Hidden Markov Model

Drug Mechanism Enrichment Analysis

Methylation array and sequencing spatial analysis methods