Package: ChromSCape
Title: Analysis of single-cell epigenomics datasets with a Shiny App
Version: 1.23.0
Authors@R: c(person(given = "Pacome",
           family = "Prompsy",
           role = c("aut", "cre"),
           email = "pacome.pr@gmail.com",
           comment = c(ORCID = "0000-0003-4375-7583")),
	   person(given = "Celine",
           family = "Vallot",
           role = c("aut"),
           email = "celine.vallot@curie.fr",
           comment = c(ORCID = "0000-0003-1601-2359")))	
Description: 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.
License: GPL-3
biocViews: ShinyApps, Software, SingleCell, ChIPSeq, ATACSeq,
        MethylSeq, Classification, Clustering, Epigenetics,
        PrincipalComponent, SingleCell, ATACSeq, ChIPSeq, Annotation,
        BatchEffect, MultipleComparison, Normalization, Pathways,
        Preprocessing, QualityControl, ReportWriting, Visualization,
        GeneSetEnrichment, DifferentialPeakCalling
VignetteBuilder: knitr
URL: https://github.com/vallotlab/ChromSCape
BugReports: https://github.com/vallotlab/ChromSCape/issues
Encoding: UTF-8
LazyData: false
Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac,
        future, igraph, bluster, httr
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles,
        shinyhelper, shinyWidgets, shinydashboardPlus, flexdashboard,
        shinycssloaders, Matrix, plotly, shinydashboard, colorRamps,
        kableExtra, viridis, batchelor, BiocParallel, parallel,
        Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV,
        stringdist, stringr, fs, qs2, 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
Depends: R (>= 4.5)
LinkingTo: Rcpp
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libbz2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev python3 xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:53:54 UTC
RemoteUrl: https://github.com/bioc/ChromSCape
RemoteRef: HEAD
RemoteSha: 7200a927807ee83c9c6b0b652a66ee476dbbce3c
NeedsCompilation: yes
Packaged: 2026-07-03 14:11:46 UTC; root
Author: Pacome Prompsy [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4375-7583>),
  Celine Vallot [aut] (ORCID: <https://orcid.org/0000-0003-1601-2359>)
Maintainer: Pacome Prompsy <pacome.pr@gmail.com>