Man pages for esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysis
| atacPipe2 | Pipeline for single replicate case-control paired-end... |
| ATACProc-class | Base class of this package |
| atacRepsPipe | Pipeline for multi-replicates case paired-end sequencing data |
| atacRepsPipe2 | Pipeline for multi-replicates case-control paired-end... |
| 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... |
| CutSitePre | Extract ATAC-seq cutting site from bed file. |
| esATAC-package | An Easy-to-use Systematic pipeline for ATACseq data analysis |
| FastQC | Quality control for ATAC-seq data. |
| FindAdapter | Use AdapterRemoval to identify adapters |
| FragLenDistr | Quality control for fragment length distribution |
| FRiPQC | Quality control for fraction of reads in peaks (FRiP) |
| getMotifInfo | Generate PFMatrix or PFMatrixList from file. |
| LibComplexQC | Quality control for library complexity |
| PeakCallingFseq | Use F-seq to call peak |
| PeakQC | Quality control for peak overlap |
| RemoveAdapter | Use AdapterRemoval to remove adapters |
| 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. |
| SamToBam | Convert sam format to bam format. |
| SamToBed | Convert SAM file to BED file |
| SingleRepReport | Final report for single group of regions |
| TSSQC | Quality control for transcription start site(TSS) reads... |
| UnzipAndMerge | Unzip and merge fastq files |
