DESCRIPTION

Package: ChromSCape
Title: Analysis of single-cell epigenomics datasets with a Shiny App
Version: 1.9.0
Authors@R: c(person(given = "Pacome",
           family = "Prompsy",
           role = c("aut", "cre"),
           email = "pacome.prompsy@curie.fr",
           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: 7.2.3
Roxygen: list(markdown = TRUE)
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
Depends: 
    R (>= 4.1)
LinkingTo: 
    Rcpp