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DESCRIPTION
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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 = "[email protected]", role = "aut"),
person("Ryan", "Corces", email = "[email protected]", role = c("aut","cre")),
person("Paulina","Paiz", role = "aut"),
person("Immanuel Abdi", email = "[email protected]", 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'