Package: esATAC 1.29.0
Zheng Wei
esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis
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.
Authors:
esATAC_1.29.0.tar.gz
esATAC_1.29.0.tgz(r-4.4-x86_64)esATAC_1.29.0.tgz(r-4.4-arm64)esATAC_1.29.0.tgz(r-4.3-x86_64)esATAC_1.29.0.tgz(r-4.3-arm64)
esATAC_1.29.0.tar.gz(r-4.5-noble)esATAC_1.29.0.tar.gz(r-4.4-noble)
esATAC_1.29.0.tgz(r-4.4-emscripten)
esATAC.pdf |esATAC.html✨
esATAC/json (API)
NEWS
| # Install 'esATAC' in R: |
| install.packages('esATAC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wzthu/esatac/issues
On BioConductor:esATAC-1.29.0(bioc 3.21)esATAC-1.28.0(bioc 3.20)
immunooncologysequencingdnaseqqualitycontrolalignmentpreprocessingcoverageatacseqdnaseseqatac-seqbioconductorpipelinecppopenjdk
Last updated 2 months agofrom:508f345865. Checks:OK: 1 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 29 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 29 2024 |
Exports:atacBam2BedatacBamSortatacBedToBigWigatacBedUtilsatacBowtie2MappingatacCutSiteCountatacExtractCutSiteatacFindAdapteratacFragLenDistratacFripQCatacGOAnalysisatacLibComplexQCatacMotifScanatacMotifScanPairatacPeakAnnoatacPeakCallingatacPeakCallingMACS2atacPeakCompatacPeakQCatacPipeatacPipe2atacQCReportatacRemoveAdapteratacRenameratacRepsPipeatacRepsPipe2atacSam2BamatacSamToBedatacSingleRepReportatacSNPAnnoatacTSSQCatacUnzipAndMergebam2bedbamsortbedToBigWigbedUtilsbowtie2MappingcutsitecountextractcutsitefindAdapterfragLenDistrfripQCgetMotifInfogoanalysislibComplexQCmotifscanmotifscanpairpeakannopeakCallingpeakCallingMACS2peakcomppeakQCqcreportremoveAdapterrenamersam2bamsamToBedsnpannotestPeakCallingMACS2tssQCunzipAndMerge
Dependencies:abindannotateAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootBSgenomebslibcachemcaToolsChIPseekerclicliprclusterProfilerCNErcodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIDelayedArraydeldirdigestDirichletMultinomialDOSEdplyrenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgridGraphicsgsongtablegtoolshighrhmshtmltoolshtmlwidgetshttrhwriterigraphinterpIRangesisobandJASPAR2018jpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemotifmatchrmunsellnlmeopensslpatchworkpillarpipeFramepkgconfigplogrplotrixplyrpngpolyclippoweRlawpracmaprettyunitsprogresspurrrpwalignqvalueR.methodsS3R.ooR.utilsR6rappdirsRbowtie2RColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrreshape2restfulrRhtslibrJavarjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesscatterpieseqLogoShortReadsnowSparseArraystringistringrSummarizedExperimentsyssystemfontsTFBSToolsTFMPvaluetibbletidyrtidyselecttidytreetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsVennDiagramviridisLitevisNetworkvroomwithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An Easy-to-use Systematic pipeline for ATACseq data analysis | esATAC-package atacPipe |
| Pipeline for single replicate case-control paired-end sequencing data | atacPipe2 |
| Base class of this package | ATACProc-class |
| Pipeline for multi-replicates case paired-end sequencing data | atacRepsPipe |
| Pipeline for multi-replicates case-control paired-end sequencing data | atacRepsPipe2 |
| Convert bam format to bed format. | atacBam2Bed atacBam2Bed,ATACProc-method bam2bed BamToBed |
| generate BigWig file from BED file | atacBedToBigWig atacBedToBigWig,ATACProc-method BedToBigWig bedToBigWig |
| process bed file with limit memory | atacBedUtils atacBedUtils,ATACProc-method BedUtils bedUtils |
| Use bowtie2 aligner to map reads to reference genome | atacBowtie2Mapping atacBowtie2Mapping,ATACProc-method Bowtie2Mapping bowtie2Mapping |
| Count cut site number in given motif region and plot footprint. | atacCutSiteCount atacCutSiteCount,ATACProc-method cutsitecount CutSiteCountR |
| Extract ATAC-seq cutting site from bed file. | atacExtractCutSite atacExtractCutSite,ATACProc-method CutSitePre extractcutsite |
| Quality control for ATAC-seq data. | atacQCReport atacQCReport,ATACProc-method FastQC qcreport |
| Use AdapterRemoval to identify adapters | atacFindAdapter atacFindAdapter,ATACProc-method FindAdapter findAdapter |
| Quality control for fragment length distribution | atacFragLenDistr atacFragLenDistr,ATACProc-method FragLenDistr fragLenDistr |
| Quality control for fraction of reads in peaks (FRiP) | atacFripQC atacFripQC,ATACProc-method FRiPQC fripQC |
| Generate PFMatrix or PFMatrixList from file. | getMotifInfo |
| Quality control for library complexity | atacLibComplexQC atacLibComplexQC,ATACProc-method LibComplexQC libComplexQC |
| Use F-seq to call peak | atacPeakCalling atacPeakCalling,ATACProc-method peakCalling PeakCallingFseq |
| Use MACS2 to call peak | atacPeakCallingMACS2 atacPeakCallingMACS2,ATACProc-method PeakCallingMACS2 peakCallingMACS2 testPeakCallingMACS2 |
| Quality control for peak overlap | atacPeakQC atacPeakQC,ATACProc-method PeakQC peakQC |
| Use AdapterRemoval to remove adapters | atacRemoveAdapter atacRemoveAdapter,ATACProc-method RemoveAdapter removeAdapter |
| Rename reads name in fastq | atacRenamer atacRenamer,ATACProc-method Renamer renamer |
| Gene Ontology Analysis | atacGOAnalysis atacGOAnalysis,ATACProc-method goanalysis RGo |
| Search Motif Position in Given Regions | atacMotifScan atacMotifScan,ATACProc-method motifscan RMotifScan |
| Search Motif Position in Given Regions | atacMotifScanPair atacMotifScanPair,ATACProc-method motifscanpair RMotifScanPair |
| Annotate ATAC-seq Peak | atacPeakAnno atacPeakAnno,ATACProc-method peakanno RPeakAnno |
| Find the overlap or differential peaks between two samples. | atacPeakComp atacPeakComp,ATACProc-method peakcomp RPeakComp |
| Find whether snps are in the given regions. | atacSNPAnno atacSNPAnno,ATACProc-method RSNPs snpanno |
| Sort bam file and rebuild bai index. | atacBamSort atacBamSort,ATACProc-method bamsort Rsortbam |
| Convert sam format to bam format. | atacSam2Bam atacSam2Bam,ATACProc-method sam2bam SamToBam |
| Convert SAM file to BED file | atacSamToBed atacSamToBed,ATACProc-method SamToBed samToBed |
| Final report for single group of regions | atacSingleRepReport atacSingleRepReport,Step-method SingleRepReport |
| Quality control for transcription start site(TSS) reads enrichment | atacTSSQC atacTSSQC,ATACProc-method TSSQC tssQC |
| Unzip and merge fastq files | atacUnzipAndMerge UnzipAndMerge unzipAndMerge |
