ChromSCape

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ChromSCape.

Analysis of single-cell epigenomics datasets with a Shiny App

Bioconductor version: 3.19

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] , Celine Vallot [aut]

Maintainer: Pacome Prompsy <pacome.prompsy at curie.fr>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChromSCape")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChromSCape")

ChromSCape	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, Annotation, BatchEffect, ChIPSeq, Classification, Clustering, DifferentialPeakCalling, Epigenetics, GeneSetEnrichment, MethylSeq, MultipleComparison, Normalization, Pathways, Preprocessing, PrincipalComponent, QualityControl, ReportWriting, ShinyApps, SingleCell, Software, Visualization
Version	1.14.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray
System Requirements
URL	https://github.com/vallotlab/ChromSCape
Bug Reports	https://github.com/vallotlab/ChromSCape/issues

Suggests	testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ChromSCape_1.14.0.tar.gz
Windows Binary (x86_64)	ChromSCape_1.14.0.zip (64-bit only)
macOS Binary (x86_64)	ChromSCape_1.14.0.tgz
macOS Binary (arm64)	ChromSCape_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChromSCape
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChromSCape
Bioc Package Browser	https://code.bioconductor.org/browse/ChromSCape/
Package Short Url	https://bioconductor.org/packages/ChromSCape/
Package Downloads Report	Download Stats