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ChromSCape

Analysis of single-cell epigenomics datasets with a Shiny App


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews ATACSeq, Annotation, BatchEffect, ChIPSeq, Classification, Clustering, DifferentialPeakCalling, Epigenetics, GeneSetEnrichment, MethylSeq, MultipleComparison, Normalization, Pathways, Preprocessing, PrincipalComponent, QualityControl, ReportWriting, ShinyApps, SingleCell, Software, Visualization
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
See More
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_1.12.0.tar.gz
Windows Binary ChromSCape_1.12.0.zip (64-bit only)
macOS Binary (x86_64) ChromSCape_1.12.0.tgz
macOS Binary (arm64) ChromSCape_1.12.0.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
Old Source Packages for BioC 3.18 Source Archive