Bioconductor Packages

Quantitative comparison of multiple ChIP-seq datasets

Quality metrics for ChIPseq data

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

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

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

R interface to a subset of OpenBabel functionalities

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

CiteFuse: multi-modal analysis of CITE-seq data

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

Judging Quality of Clustering Methods using Mutual Information

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

Create Copy-Number Plots using karyoploteR functionality

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

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

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

Finds DAMEs - Differential Allelicly MEthylated regions

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

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 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