Package: esATAC
Type: Package
Title: An Easy-to-use Systematic pipeline for ATACseq data analysis
Version: 1.31.1
Date: 2025-07-22
Author: Zheng Wei, Wei Zhang
Maintainer: Zheng Wei <wzweizheng@qq.com>
Description: This package provides a framework and complete preset pipeline for
    quantification and analysis of ATAC-seq Reads. It covers raw sequencing
    reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads
    file operations (SAM, BAM, and BED files), peak calling (F-seq), genome 
    annotations (Motif, GO, SNP analysis) and quality control report. The package 
    is managed by dataflow graph. It is easy for user to pass variables seamlessly
    between processes and understand the workflow. Users can process FASTQ files 
    through end-to-end preset pipeline which produces a pretty HTML report for 
    quality control and preliminary statistical results, or customize workflow 
    starting from any intermediate stages with esATAC functions easily and flexibly. 
Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame
License: GPL-3 | file LICENSE
Encoding: UTF-8
Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer,
        ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph,
        rJava, magrittr, digest, BSgenome, AnnotationDbi,
        GenomicAlignments, GenomicFeatures, R.utils, Seqinfo,
        BiocGenerics, S4Vectors, IRanges, rmarkdown, tools,
        VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics,
        stats, utils, parallel, corrplot, BiocManager, motifmatchr
Suggests: BSgenome.Hsapiens.UCSC.hg19,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat,
        webshot, prettydoc
LinkingTo: Rcpp
SystemRequirements: C++11
Collate: ATACProc.R BamToBed.R BedToBigWig.R BedUtils.R ConfigVal.R
        CppInterface.R CutSiteCountR.R CutSitePre.R FRiPQC.R FastQC.R
        FregLenDistribute.R FindAdapter.R JavaExports.R JavaInterface.R
        LibComplexQC.R Mapping.R Methods.R PeakCallingFseq.R
        PeakCallingMACS2.R PeakQC.R RGo.R RMotifScan.R RPeakAnno.R
        RPeakComp.R RSNPs.R RcppExports.R RemoveAdapter.R Renamer.R
        Rsortbam.R SamToBam.R SamToBed.R TSSQC.R UnzipAndMerge.R
        onLoad.R RMotifScanPair.R utilities.R SingleRepReport.R
biocViews: ImmunoOncology, Sequencing, DNASeq, QualityControl,
        Alignment, Preprocessing, Coverage, ATACSeq, DNaseSeq
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: yes
URL: https://github.com/wzthu/esATAC
BugReports: https://github.com/wzthu/esATAC/issues
git_url: https://git.bioconductor.org/packages/esATAC
git_branch: devel
git_last_commit: 999ba9f
git_last_commit_date: 2025-07-23
Repository: Bioconductor 3.22
Date/Publication: 2025-07-23
Packaged: 2025-07-23 23:01:01 UTC; biocbuild
Built: R 4.5.1; x86_64-w64-mingw32; 2025-07-24 13:06:33 UTC; windows
Archs: x64
