ChromSCape

This is the development version of ChromSCape; for the stable release version, see ChromSCape.

Analysis of single-cell epigenomics datasets with a Shiny App

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DOI: 10.18129/B9.bioc.ChromSCape

Bioconductor version: Development (3.23)

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Author: Pacome Prompsy [aut, cre] ORCID iD ORCID: 0000-0003-4375-7583 , Celine Vallot [aut] ORCID iD ORCID: 0000-0003-1601-2359

Maintainer: Pacome Prompsy <pacome.pr at gmail.com>

Citation (from within R, enter citation("ChromSCape")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ChromSCape")

For older versions of R, please refer to the appropriate Bioconductor release.