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

Documentation for package ‘esATAC’ version 1.16.0

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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.
atacFindAdapter	Use AdapterRemoval to identify adapters
atacFindAdapter-method	Use AdapterRemoval to identify adapters
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
ATACProc-class	Base class of this package
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
atacSingleRepReport	Final report for single group of regions
atacSingleRepReport-method	Final report for single group of regions
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 --

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.
FindAdapter	Use AdapterRemoval to identify adapters
findAdapter	Use AdapterRemoval to identify adapters
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 --

getMotifInfo	Generate PFMatrix or PFMatrixList from file.
goanalysis	Gene Ontology Analysis

-- 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

-- 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
SingleRepReport	Final report for single group of regions
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