Package: esATAC
Type: Package
Title: An Easy-to-use Systematic pipeline for ATACseq data analysis
Version: 1.35.0
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 cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libgsl0-dev default-jdk
        libbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:46:56 UTC
RemoteUrl: https://github.com/bioc/esATAC
RemoteRef: HEAD
RemoteSha: 309de8b345694d4cd62029a048261aed01655d47
Packaged: 2026-05-28 14:58:17 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2026-05-28 15:04:53 UTC; windows
Archs: x64
