{ "_id": "6a4a69b31e9cffeb4b833a5f", "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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