ChromSCape

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see ChromSCape.

Analysis of single-cell epigenomics datasets with a Shiny App

Bioconductor version: 3.18

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

Need some help? Ask on the Bioconductor Support site!

Details

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

Suggests testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr

Linking To Rcpp

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