Package: ChromSCape
Title: Analysis of single-cell epigenomics datasets with a Shiny App
Version: 1.16.0
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: 7.1.2
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
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_20
git_last_commit: 243f2f8
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: yes
Packaged: 2024-10-30 00:00:14 UTC; biocbuild
Author: Pacome Prompsy [aut, cre] (<https://orcid.org/0000-0003-4375-7583>),
  Celine Vallot [aut] (<https://orcid.org/0000-0003-1601-2359>)
Maintainer: Pacome Prompsy <pacome.prompsy@curie.fr>
Built: R 4.4.2; x86_64-conda-linux-gnu; 2025-01-03 20:30:48 UTC; unix
