Man pages for esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysis

atacPipe2Pipeline for single replicate case-control paired-end...
ATACProc-classBase class of this package
atacRepsPipePipeline for multi-replicates case paired-end sequencing data
atacRepsPipe2Pipeline for multi-replicates case-control paired-end...
BamToBedConvert bam format to bed format.
BedToBigWiggenerate BigWig file from BED file
BedUtilsprocess bed file with limit memory
Bowtie2MappingUse bowtie2 aligner to map reads to reference genome
CutSiteCountRCount cut site number in given motif region and plot...
CutSitePreExtract ATAC-seq cutting site from bed file.
esATAC-packageAn Easy-to-use Systematic pipeline for ATACseq data analysis
FastQCQuality control for ATAC-seq data.
FindAdapterUse AdapterRemoval to identify adapters
FragLenDistrQuality control for fragment length distribution
FRiPQCQuality control for fraction of reads in peaks (FRiP)
getMotifInfoGenerate PFMatrix or PFMatrixList from file.
LibComplexQCQuality control for library complexity
PeakCallingFseqUse F-seq to call peak
PeakQCQuality control for peak overlap
RemoveAdapterUse AdapterRemoval to remove adapters
RenamerRename reads name in fastq
RGoGene Ontology Analysis
RMotifScanSearch Motif Position in Given Regions
RMotifScanPairSearch Motif Position in Given Regions
RPeakAnnoAnnotate ATAC-seq Peak
RPeakCompFind the overlap or differential peaks between two samples.
RSNPsFind whether snps are in the given regions.
RsortbamSort bam file and rebuild bai index.
SamToBamConvert sam format to bam format.
SamToBedConvert SAM file to BED file
SingleRepReportFinal report for single group of regions
TSSQCQuality control for transcription start site(TSS) reads...
UnzipAndMergeUnzip and merge fastq files
esATAC documentation built on April 29, 2020, 5:50 a.m.