ATACProc-class          Methods for ATACProc objects
BamToBed                Convert bam format to bed format.
BedToBigWig             generate BigWig file from BED file
BedUtils                process bed file with limit memory
Bowtie2Mapping          Use bowtie2 aligner to map reads to reference
                        genome
CutSiteCountR           Count cut site number in given motif region and
                        plot footprint.
CutSitePre              Extract ATAC-seq cutting site from bed file.
FRiPQC                  Quality control for fraction of reads in peaks
                        (FRiP)
FastQC                  Quality control for ATAC-seq data.
FragLenDistr            Quality control for fragment length
                        distribution
LibComplexQC            Quality control for library complexity
PeakCallingFseq         Use F-seq to call peak
PeakQC                  Quality control for peak overlap
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.
RemoveAdapter           Use AdapterRemoval to remove adapters
Renamer                 Rename reads name in fastq
Rsortbam                Sort bam file and rebuild bai index.
SamToBam                Convert sam format to bam format.
SamToBed                Convert SAM file to BED file
TSSQC                   Quality control for transcription start
                        site(TSS) reads enrichment
UnzipAndMerge           Unzip and merge fastq files
atacPipe2               Pipeline for single replicate case-control
                        paired-end sequencing data
atacRepsPipe            Pipeline for multi-replicates case paired-end
                        sequencing data
atacRepsPipe2           Pipeline for multi-replicates case-control
                        paired-end sequencing data
configureValue          Global parameters configure
esATAC-package          An Easy-to-use Systematic pipeline for ATACseq
                        data analysis
getMotifInfo            Generate PFMatrix or PFMatrixList from file.
