ChromSCape

DOI: 10.18129/B9.bioc.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

Bioconductor version: Development (3.17)

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>

Installation

To install this package, start R (version "4.3") 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.

Documentation

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

browseVignettes("ChromSCape")

 

HTML	R Script	ChromSCape
PDF		Reference Manual

Details

biocViews	ATACSeq, Annotation, BatchEffect, ChIPSeq, Classification, Clustering, DifferentialPeakCalling, Epigenetics, GeneSetEnrichment, MethylSeq, MultipleComparison, Normalization, Pathways, Preprocessing, PrincipalComponent, QualityControl, ReportWriting, ShinyApps, SingleCell, Software, Visualization
Version	1.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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
LinkingTo	Rcpp
Suggests	testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr
SystemRequirements
Enhances
URL	https://github.com/vallotlab/ChromSCape
BugReports	https://github.com/vallotlab/ChromSCape/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ChromSCape_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/ChromSCape
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChromSCape
Package Short Url	https://bioconductor.org/packages/ChromSCape/
Package Downloads Report	Download Stats