Package: ChromSCape Title: Analysis of single-cell epigenomics datasets with a Shiny App Version: 1.19.0 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