{ "_id": "6a192ce9acfb0bcc41dcf081", "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 ", "Description": "This package provides a framework and complete preset\npipeline for quantification and analysis of ATAC-seq Reads. It\ncovers raw sequencing reads preprocessing (FASTQ files), reads\nalignment (Rbowtie2), aligned reads file operations (SAM, BAM,\nand BED files), peak calling (F-seq), genome annotations\n(Motif, GO, SNP analysis) and quality control report. The\npackage is managed by dataflow graph. It is easy for user to\npass variables seamlessly between processes and understand the\nworkflow. Users can process FASTQ files through end-to-end\npreset pipeline which produces a pretty HTML report for quality\ncontrol and preliminary statistical results, or customize\nworkflow starting from any intermediate stages with esATAC\nfunctions easily and flexibly.", "License": "GPL-3 | file LICENSE", "Encoding": "UTF-8", "SystemRequirements": "C++11", "Collate": "ATACProc.R BamToBed.R BedToBigWig.R BedUtils.R ConfigVal.R\nCppInterface.R CutSiteCountR.R CutSitePre.R FRiPQC.R FastQC.R\nFregLenDistribute.R FindAdapter.R JavaExports.R JavaInterface.R\nLibComplexQC.R Mapping.R Methods.R PeakCallingFseq.R\nPeakCallingMACS2.R PeakQC.R RGo.R RMotifScan.R RPeakAnno.R\nRPeakComp.R RSNPs.R RcppExports.R RemoveAdapter.R Renamer.R\nRsortbam.R SamToBam.R SamToBed.R TSSQC.R UnzipAndMerge.R\nonLoad.R RMotifScanPair.R utilities.R SingleRepReport.R", "biocViews": "ImmunoOncology, Sequencing, DNASeq, QualityControl,\nAlignment, Preprocessing, Coverage, ATACSeq, DNaseSeq", "VignetteBuilder": "knitr", 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plot footprint.", "topics": [ "atacCutSiteCount", "atacCutSiteCount,ATACProc-method", "cutsitecount", "CutSiteCountR" ] }, { "page": "CutSitePre", "title": "Extract ATAC-seq cutting site from bed file.", "topics": [ "atacExtractCutSite", "atacExtractCutSite,ATACProc-method", "CutSitePre", "extractcutsite" ] }, { "page": "FastQC", "title": "Quality control for ATAC-seq data.", "topics": [ "atacQCReport", "atacQCReport,ATACProc-method", "FastQC", "qcreport" ] }, { "page": "FindAdapter", "title": "Use AdapterRemoval to identify adapters", "topics": [ "atacFindAdapter", "atacFindAdapter,ATACProc-method", "FindAdapter", "findAdapter" ] }, { "page": "FragLenDistr", "title": "Quality control for fragment length distribution", "topics": [ "atacFragLenDistr", "atacFragLenDistr,ATACProc-method", "FragLenDistr", "fragLenDistr" ] }, { "page": "FRiPQC", "title": "Quality control for fraction of reads in peaks (FRiP)", "topics": [ "atacFripQC", "atacFripQC,ATACProc-method", "FRiPQC", "fripQC" ] }, { "page": "getMotifInfo", "title": "Generate PFMatrix or PFMatrixList from file.", "topics": [ "getMotifInfo" ] }, { "page": "LibComplexQC", "title": "Quality control for library complexity", "topics": [ "atacLibComplexQC", "atacLibComplexQC,ATACProc-method", "LibComplexQC", "libComplexQC" ] }, { "page": "PeakCallingFseq", "title": "Use F-seq to call peak", "topics": [ "atacPeakCalling", "atacPeakCalling,ATACProc-method", "peakCalling", "PeakCallingFseq" ] }, { "page": "PeakCallingMACS2", "title": "Use MACS2 to call peak", "topics": [ "atacPeakCallingMACS2", "atacPeakCallingMACS2,ATACProc-method", "PeakCallingMACS2", "peakCallingMACS2", "testPeakCallingMACS2" ] }, { "page": "PeakQC", "title": "Quality control for peak overlap", "topics": [ "atacPeakQC", "atacPeakQC,ATACProc-method", "PeakQC", "peakQC" ] }, { "page": "RemoveAdapter", "title": "Use AdapterRemoval to remove adapters", "topics": [ "atacRemoveAdapter", "atacRemoveAdapter,ATACProc-method", "RemoveAdapter", "removeAdapter" ] }, 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