DESCRIPTION

Package: SnapATAC
Version: 1.0.0
Date: 2019-03-28
Title: Single Nucleus Analysis Package for ATAC-Seq
Authors@R: person(given = "Rongxin", family = "Fang", email = "r4fang@gmail.com", role = c("aut", "cre"))
Description: A fast and accurate analysis toolkit for single cell ATAC-seq. Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and reveal cell-type specific regulatory landscapes. However, the exceeding data sparsity has posed unique challenges for the data analysis. SnapATAC is an end-to-end bioinformatics pipeline for analyzing large-scale single cell ATAC-seq data which includes quality control, normalization, clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data. See Preissl S, Fang R, et al (2018) <doi:10.1038/s41593-018-0079-3> for more details.
biocViews: Software
URL: https://github.com/r3fang/SnapATAC
BugReports: https://github.com/r3fang/SnapATAC/issues
Depends:
	R (>= 3.4.0),
	Matrix (>= 1.2.14),
	rhdf5 (>= 2.20.0),
	methods
Imports:
	GenomicRanges,
	IRanges,
	stats,
	raster,
	irlba,
	Rtsne,
	edgeR,
	RANN,
	scales,
	RColorBrewer,
	parallel,
	foreach,
	doParallel,
	igraph,
	plyr,
	bigmemory,
	grDevices, 
	graphics, 
	utils,
	viridis
Suggests:
	umap,
	chromVAR,
	leiden,
	lda,
	doSNOW
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Collate: 
    'createGmat.R'
    'createPmat.R'
    'data.R'
    'dimReduct-class.R'
    'findDARs.R'
    'jaccard-class.R'
    'kgraph-class.R'
    'makeBinary.R'
    'utilities.R'
    'normJaccard.R'
    'plottings-utilities.R'
    'plottings.R'
    'predictGenePeakPair.R'
    'runChromVAR.R'
    'runClusters.R'
    'runDimReduct.R'
    'runHarmony.R'
    'runHomer.R'
    'runJaccard.R'
    'snap-class.R'
    'runKNN.R'
    'runLDA.R'
    'runLDM.R'
    'runLSA.R'
    'runMACS.R'
    'runMagic.R'
    'runSnapAddPmat.R'
    'runViz.R'
    'scaleCountMatrix.R'
    'snap-utilities.R'
    'snapToSeurat.R'