Package: ArchR
Type: Package
Date: 2025-01-19
Title: Analyzing single-cell regulatory chromatin in R.
Version: 1.0.3
Authors@R: c(
    person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = "aut"),
    person("Ryan", "Corces", email = "ryan.corces@gladstone.ucsf.edu", role = c("aut","cre")),
    person("Paulina","Paiz", role = "aut"),
    person("Immanuel Abdi", email = "iabdi@stanford.edu", role = c("aut", "ctb")))
Description: This package is designed to streamline scATAC analyses in
        R.
Roxygen: list(markdown = TRUE)
License: MIT
LinkingTo: Rcpp, RcppArmadillo
LazyData: TRUE
URL: https://www.ArchRProject.com
RoxygenNote: 7.3.2
Encoding: UTF-8
Imports: BiocGenerics, Biostrings, chromVAR, chromVARmotifs,
        ComplexHeatmap, data.table, devtools, GenomicRanges, ggplot2,
        ggrepel, gridExtra, gtable, gtools, harmony, magrittr, Matrix,
        matrixStats, motifmatchr, nabor, plyr, presto, Rcpp (>=
        0.12.16), RcppArmadillo, rhdf5, Rsamtools, S4Vectors (>=
        0.9.25), Seurat, SeuratObject, sparseMatrixStats, stringr,
        SummarizedExperiment, uwot
Depends:
Suggests: Cairo, DESeq2, edgeR, GenomicFeatures, ggridges, ggseqlogo,
        hexbin, leiden, limma, monocle3, pdftools, pheatmap,
        rhandsontable, scran, shiny, shinythemes, slingshot, testthat
Remotes: GreenleafLab/chromVARmotifs, cole-trapnell-lab/monocle3,
        immunogenomics/presto
Collate: 'AllClasses.R' 'AnnotationGenome.R' 'AnnotationPeaks.R'
        'ArchRBrowser.R' 'ArchRHeatmap.R' 'ArrowRead.R' 'ArrowUtils.R'
        'ArrowWrite.R' 'BulkProjection.R' 'Clustering.R'
        'ColorPalettes.R' 'CreateArrow.R' 'DoubletsScores.R'
        'Embedding.R' 'FilterCells.R' 'Footprinting.R' 'GRangesUtils.R'
        'GgplotUtils.R' 'GlobalDefaults.R' 'GroupCoverages.R'
        'HelperUtils.R' 'GroupExport.R' 'Harmony.R' 'HiddenUtils.R'
        'Imputation.R' 'InputData.R' 'IntegrativeAnalysis.R'
        'IterativeLSI.R' 'LoggerUtils.R' 'MarkerFeatures.R'
        'MatrixDeviations.R' 'MatrixFeatures.R'
        'MatrixGeneExpression.R' 'MatrixGeneScores.R' 'MatrixTiles.R'
        'ModuleScore.R' 'MultiModal.R' 'ProjectMethods.R'
        'QualityControl.R' 'RNAIntegration.R' 'RcppExports.R'
        'ReproduciblePeakSet.R' 'SparseUtils.R' 'Trajectory.R'
        'ValidationUtils.R' 'VisualizeData.R'
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev git libglpk-dev make libgsl0-dev libharfbuzz-dev
        libbz2-dev libgit2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev
        libssl-dev perl python3 libx11-dev xz-utils zlib1g-dev
Repository: https://tttpob.r-universe.dev
Date/Publication: 2025-02-18 21:19:00 UTC
RemoteUrl: https://github.com/GreenleafLab/ArchR
RemoteRef: HEAD
RemoteSha: 6feec354ad6c8052ddbc4626a2ca2d858ed465bf
NeedsCompilation: yes
Packaged: 2026-10-04 14:48:17 UTC; root
Author: Jeffrey Granja [aut],
  Ryan Corces [aut, cre],
  Paulina Paiz [aut],
  Immanuel Abdi [aut, ctb]
Maintainer: Ryan Corces <ryan.corces@gladstone.ucsf.edu>