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

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Documentation for package ‘esATAC’ version 1.12.0

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A B C E F G 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.
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