Bioconductor Packages

Cheminformatics Toolkit for R

Heat map plotting by genome coordinate

Analysis of single-cell epigenomics datasets with a Shiny App

End-to-End Analysis of Small RNA-Seq Data from Viroids

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

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

Complexome Profiling Analysis package

Automated detection tool for spillover errors

Make Complex Heatmaps

Creating and Using (Chemical) Compound Annotation Databases

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

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

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Low Dimensions projection of cytometry samples

Automation and visualization of flow cytometry data analysis pipelines

GUI's for visualization of flow cytometry data analysis pipelines

Tools for the Differential Analysis of Proteins Abundance with R

Denoising Algorithm based on Relevance network Topology

Differential Composition Analysis Transformed by a Similarity matrix

Tools for curating, analyzing, and manipulating biological sequences

Two-sample tests on a graph

Report of DEG analysis

Identify Differentially Expressed Genes from RNA-seq data

Differential gene expression analysis based on the negative binomial distribution

DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions

Inference of differential exon usage in RNA-Seq

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

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

Methylation array and sequencing spatial analysis methods