Bioconductor Packages

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

VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Functional connections between drugs, genes and diseases as revealed by common gene-expression changes

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

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Low Dimensions projection of cytometry samples

DNA methylation-based machine learning models

Finds DAMEs - Differential Allelicly MEthylated regions

Denoising Algorithm based on Relevance network Topology

Tools for curating, analyzing, and manipulating biological sequences

Differential gene expression data formats converter

Two-sample tests on a graph

Report of DEG analysis

Identify Differentially Expressed Genes from RNA-seq data

Identifies differentially expressed genes with respect to other local genes

Differential Enrichment Scan 2

Differential gene expression analysis based on the negative binomial distribution

Differential Expressed Windows Based on Negative Binomial Distribution

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

Gene Selection

Diffuse large B-cell lymphoma expression data

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated CpG using Hidden Markov Model

Differentially Methylated Regions Caller

Methylation array and sequencing spatial analysis methods

Data Package for DMRcate

Example DNAm Data for DMRsegal

DNA Cyclizability Prediction