DESCRIPTION

Package: ArchR
Type: Package
Date: 2020-11-23
Title: Analyzing single-cell regulatory chromatin in R.
Version: 1.0.1
Authors@R: c(
    person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = c("aut","cre")),
    person("Ryan", "Corces", role = "aut"))
Description: This package is designed to streamline scATAC analyses in R.
Roxygen: list(markdown = TRUE)
License: GPL (>= 2)
LinkingTo: Rcpp
LazyData: TRUE
RoxygenNote: 7.1.1
Encoding: UTF-8
Imports:
    Rcpp (>= 0.12.16),
    matrixStats,
    plyr,
    nabor,
    motifmatchr,
    chromVAR,
    uwot,
    ggrepel,
    Rsamtools,
    gtable,
    gtools,
    stringr,
    grid,
    gridExtra,
    Biostrings,
    ComplexHeatmap
Depends:
    ggplot2,
    SummarizedExperiment,
    data.table,
    Matrix,
    rhdf5,
    magrittr,
    S4Vectors (>= 0.9.25),
    BiocGenerics,
    GenomicRanges
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'
    'Trajectory.R'
    'ValidationUtils.R'
    'VisualizeData.R'