Package: esATAC
Type: Package
Title: An Easy-to-use Systematic pipeline for ATACseq data analysis
Version: 1.32.0
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
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libgsl0-dev default-jdk libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:42:12 UTC
RemoteUrl: https://github.com/bioc/esATAC
RemoteRef: RELEASE_3_22
RemoteSha: 6d7ce39608e9541b1455060ba5a8c36fa7c8864f
Packaged: 2025-11-11 15:44:09 UTC; root
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 15:59:46 UTC; windows
Archs: x64
