# An Easy-to-use Systematic pipeline for ATACseq data analysis

## Documentation for package ‘esATAC’ version 1.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E F G I L M P Q R S T U

esATAC-package | An Easy-to-use Systematic pipeline for ATACseq data analysis

## -- A --

atacBam2Bed | Convert bam format to bed format.
atacBam2Bed-method | Convert bam format to bed format.
atacBamSort | Sort bam file and rebuild bai index.
atacBamSort-method | Sort bam file and rebuild bai index.
atacBedToBigWig | generate BigWig file from BED file
atacBedToBigWig-method | generate BigWig file from BED file
atacBedUtils | process bed file with limit memory
atacBedUtils-method | process bed file with limit memory
atacBowtie2Mapping | Use bowtie2 aligner to map reads to reference genome
atacBowtie2Mapping-method | Use bowtie2 aligner to map reads to reference genome
atacCutSiteCount | Count cut site number in given motif region and plot footprint.
atacCutSiteCount-method | Count cut site number in given motif region and plot footprint.
atacExtractCutSite | Extract ATAC-seq cutting site from bed file.
atacExtractCutSite-method | Extract ATAC-seq cutting site from bed file.
atacFragLenDistr | Quality control for fragment length distribution
atacFragLenDistr-method | Quality control for fragment length distribution
atacFripQC | Quality control for fraction of reads in peaks (FRiP)
atacFripQC-method | Quality control for fraction of reads in peaks (FRiP)
atacGOAnalysis | Gene Ontology Analysis
atacGOAnalysis-method | Gene Ontology Analysis
atacLibComplexQC | Quality control for library complexity
atacLibComplexQC-method | Quality control for library complexity
atacMotifScan | Search Motif Position in Given Regions
atacMotifScan-method | Search Motif Position in Given Regions
atacMotifScanPair | Search Motif Position in Given Regions
atacMotifScanPair-method | Search Motif Position in Given Regions
atacPeakAnno | Annotate ATAC-seq Peak
atacPeakAnno-method | Annotate ATAC-seq Peak
atacPeakCalling | Use F-seq to call peak
atacPeakCalling-method | Use F-seq to call peak
atacpeakComp | Find the overlap or differential peaks between two samples.
atacpeakComp-method | Find the overlap or differential peaks between two samples.
atacPeakQC | Quality control for peak overlap
atacPeakQC-method | Quality control for peak overlap
atacPipe | An Easy-to-use Systematic pipeline for ATACseq data analysis
atacPipe2 | Pipeline for single replicate case-control paired-end sequencing data
atacPrintMap | Methods for ATACProc objects
atacPrintMap-method | Methods for ATACProc objects
ATACProc-class | Methods for ATACProc objects
atacQCReport | Quality control for ATAC-seq data.
atacQCReport-method | Quality control for ATAC-seq data.
atacRemoveAdapter | Use AdapterRemoval to remove adapters
atacRemoveAdapter-method | Use AdapterRemoval to remove adapters
atacRenamer | Rename reads name in fastq
atacRenamer-method | Rename reads name in fastq
atacRepsPipe | Pipeline for multi-replicates case paired-end sequencing data
atacRepsPipe2 | Pipeline for multi-replicates case-control paired-end sequencing data
atacSam2Bam | Convert sam format to bam format.
atacSam2Bam-method | Convert sam format to bam format.
atacSamToBed | Convert SAM file to BED file
atacSamToBed-method | Convert SAM file to BED file
atacSNPAnno | Find whether snps are in the given regions.
atacSNPAnno-method | Find whether snps are in the given regions.
atacTSSQC | Quality control for transcription start site(TSS) reads enrichment
atacTSSQC-method | Quality control for transcription start site(TSS) reads enrichment
atacUnzipAndMerge | Unzip and merge fastq files

## -- B --

bam2bed | Convert bam format to bed format.
bamsort | Sort bam file and rebuild bai index.
BamToBed | Convert bam format to bed format.
BedToBigWig | generate BigWig file from BED file
bedToBigWig | generate BigWig file from BED file
BedUtils | process bed file with limit memory
bedUtils | process bed file with limit memory
Bowtie2Mapping | Use bowtie2 aligner to map reads to reference genome
bowtie2Mapping | Use bowtie2 aligner to map reads to reference genome

## -- C --

clearProcCache | Methods for ATACProc objects
clearProcCache-method | Methods for ATACProc objects
configureValue | Global parameters configure
cutsitecount | Count cut site number in given motif region and plot footprint.
CutSiteCountR | Count cut site number in given motif region and plot footprint.
CutSitePre | Extract ATAC-seq cutting site from bed file.

## -- E --

extractcutsite | Extract ATAC-seq cutting site from bed file.

## -- F --

FastQC | Quality control for ATAC-seq data.
FragLenDistr | Quality control for fragment length distribution
fragLenDistr | Quality control for fragment length distribution
FRiPQC | Quality control for fraction of reads in peaks (FRiP)
fripQC | Quality control for fraction of reads in peaks (FRiP)

## -- G --

getAllConfigure | Global parameters configure
getConfigure | Global parameters configure
getMotifInfo | Generate PFMatrix or PFMatrixList from file.
getParam | Methods for ATACProc objects
getParam-method | Methods for ATACProc objects
getParamItems | Methods for ATACProc objects
getParamItems-method | Methods for ATACProc objects
getProcName | Methods for ATACProc objects
getProcName-method | Methods for ATACProc objects
getReportItems | Methods for ATACProc objects
getReportItems-method | Methods for ATACProc objects
getReportVal | Methods for ATACProc objects
getReportVal-method | Methods for ATACProc objects
goanalysis | Gene Ontology Analysis

## -- I --

isReady | Methods for ATACProc objects
isReady-method | Methods for ATACProc objects
isSingleEnd | Methods for ATACProc objects
isSingleEnd-method | Methods for ATACProc objects

## -- L --

LibComplexQC | Quality control for library complexity
libComplexQC | Quality control for library complexity

## -- M --

motifscan | Search Motif Position in Given Regions
motifscanpair | Search Motif Position in Given Regions

## -- P --

peakanno | Annotate ATAC-seq Peak
peakCalling | Use F-seq to call peak
PeakCallingFseq | Use F-seq to call peak
peakcomp | Find the overlap or differential peaks between two samples.
PeakQC | Quality control for peak overlap
peakQC | Quality control for peak overlap
printMap | Methods for ATACProc objects
process | Methods for ATACProc objects
process-method | Methods for ATACProc objects

## -- Q --

qcreport | Quality control for ATAC-seq data.

## -- R --

RemoveAdapter | Use AdapterRemoval to remove adapters
removeAdapter | Use AdapterRemoval to remove adapters
Renamer | Rename reads name in fastq
renamer | Rename reads name in fastq
RGo | Gene Ontology Analysis
RMotifScan | Search Motif Position in Given Regions
RMotifScanPair | Search Motif Position in Given Regions
RPeakAnno | Annotate ATAC-seq Peak
RPeakComp | Find the overlap or differential peaks between two samples.
RSNPs | Find whether snps are in the given regions.
Rsortbam | Sort bam file and rebuild bai index.

## -- S --

sam2bam | Convert sam format to bam format.
SamToBam | Convert sam format to bam format.
SamToBed | Convert SAM file to BED file
samToBed | Convert SAM file to BED file
setConfigure | Global parameters configure
snpanno | Find whether snps are in the given regions.

## -- T --

TSSQC | Quality control for transcription start site(TSS) reads enrichment
tssQC | Quality control for transcription start site(TSS) reads enrichment

## -- U --

UnzipAndMerge | Unzip and merge fastq files
unzipAndMerge | Unzip and merge fastq files