API for esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysis
| Global functions | |
|---|---|
| .CutSiteCount | Source code |
| .CutSite_call | Source code |
| .bedOprUtils_call | Source code |
| .chr_separate_call | Source code |
| .fseq_call | Source code |
| .lib_complex_qc_call | Source code |
| .onLoad | Source code |
| .qa_ShortRead | Source code |
| .renamer_call | Source code |
| .sam2bed_call | Source code |
| .sam2bed_merge_call | Source code |
| ATACProc-class | Man page |
| BamToBed | Man page |
| BedToBigWig | Man page |
| BedUtils | Man page |
| Bowtie2Mapping | Man page |
| ChrDivi_wrapper | Source code |
| CutCountPre_wrapper | Source code |
| CutSiteCountR | Man page |
| CutSiteCount_wrapper | Source code |
| CutSitePre | Man page |
| FRiPQC | Man page |
| FastQC | Man page |
| FindAdapter | Man page |
| FragLenDistr | Man page |
| LibComplexQC | Man page |
| PeakCallingFseq | Man page |
| PeakQC | Man page |
| RGo | Man page |
| RMotifScan | Man page |
| RMotifScanPair | Man page |
| RPeakAnno | Man page |
| RPeakComp | Man page |
| RSNPs | Man page |
| R_sam2bed_merge_wrapper | Source code |
| R_sam2bed_wrapper | Source code |
| RemoveAdapter | Man page |
| Renamer | Man page |
| Rsortbam | Man page |
| SamToBam | Man page |
| SamToBed | Man page |
| SingleRepReport | Man page |
| TSSQC | Man page |
| UnzipAndMerge | Man page |
| atacBam2Bed | Man page |
| atacBam2Bed,ATACProc-method | Man page |
| atacBamSort | Man page |
| atacBamSort,ATACProc-method | Man page |
| atacBedToBigWig | Man page |
| atacBedToBigWig,ATACProc-method | Man page |
| atacBedUtils | Man page |
| atacBedUtils,ATACProc-method | Man page |
| atacBowtie2Mapping | Man page |
| atacBowtie2Mapping,ATACProc-method | Man page |
| atacCutSiteCount | Man page |
| atacCutSiteCount,ATACProc-method | Man page |
| atacExtractCutSite | Man page |
| atacExtractCutSite,ATACProc-method | Man page |
| atacFindAdapter | Man page |
| atacFindAdapter,ATACProc-method | Man page |
| atacFragLenDistr | Man page |
| atacFragLenDistr,ATACProc-method | Man page |
| atacFripQC | Man page |
| atacFripQC,ATACProc-method | Man page |
| atacGOAnalysis | Man page |
| atacGOAnalysis,ATACProc-method | Man page |
| atacLibComplexQC | Man page |
| atacLibComplexQC,ATACProc-method | Man page |
| atacMotifScan | Man page |
| atacMotifScan,ATACProc-method | Man page |
| atacMotifScanPair | Man page |
| atacMotifScanPair,ATACProc-method | Man page |
| atacPeakAnno | Man page |
| atacPeakAnno,ATACProc-method | Man page |
| atacPeakCalling | Man page |
| atacPeakCalling,ATACProc-method | Man page |
| atacPeakQC | Man page |
| atacPeakQC,ATACProc-method | Man page |
| atacPipe | Man page Source code |
| atacPipe2 | Man page Source code |
| atacQCReport | Man page |
| atacQCReport,ATACProc-method | Man page |
| atacRemoveAdapter | Man page |
| atacRemoveAdapter,ATACProc-method | Man page |
| atacRenamer | Man page |
| atacRenamer,ATACProc-method | Man page |
| atacRepsPipe | Man page Source code |
| atacRepsPipe2 | Man page Source code |
| atacSNPAnno | Man page |
| atacSNPAnno,ATACProc-method | Man page |
| atacSam2Bam | Man page |
| atacSam2Bam,ATACProc-method | Man page |
| atacSamToBed | Man page |
| atacSamToBed,ATACProc-method | Man page |
| atacSingleRepReport | Man page |
| atacSingleRepReport,Step-method | Man page |
| atacTSSQC | Man page |
| atacTSSQC,ATACProc-method | Man page |
| atacUnzipAndMerge | Man page Source code |
| atacpeakComp | Man page |
| atacpeakComp,ATACProc-method | Man page |
| bam2bed | Man page Source code |
| bamsort | Man page Source code |
| bedOprUtils | Source code |
| bedToBigWig | Man page Source code |
| bedUtils | Man page Source code |
| bowtie2Mapping | Man page Source code |
| calcQaInformation | Source code |
| checkAndInstall | Source code |
| checkAndInstallBSgenomeTestgenome | Source code |
| checkAndInstallBt2Idx | Source code |
| checkFilePathExist | Source code |
| checkParam | Source code |
| compressedFileFormat | Source code |
| consolidateFileExtensions | Source code |
| cutsitecount | Man page Source code |
| downloadAndGunzip | Source code |
| downloadBlacklist | Source code |
| downloadDHS | Source code |
| downloadSNP | Source code |
| esATAC-package | Man page |
| extractcutsite | Man page Source code |
| fastxrenamer | Source code |
| findAdapter | Man page Source code |
| fragLenDistr | Man page Source code |
| fripQC | Man page Source code |
| fseq | Source code |
| getBinsReadsCount | Source code |
| getMotifInfo | Man page Source code |
| getPer | Source code |
| getRshow | Source code |
| getSuffix0 | Source code |
| getSuffixlessFileName0 | Source code |
| getVM | Source code |
| getVMR | Source code |
| getVMRShow | Source code |
| getVMShow | Source code |
| getf | Source code |
| goanalysis | Man page Source code |
| libComplexQC | Man page Source code |
| lib_complex_qc | Source code |
| listToFrame | Source code |
| mergeFile | Source code |
| mid_interval | Source code |
| motifscan | Man page Source code |
| motifscanpair | Man page Source code |
| peakCalling | Man page Source code |
| peakQC | Man page Source code |
| peakanno | Man page Source code |
| peakcomp | Man page Source code |
| plotDuplicated | Source code |
| plotNuclByCycle | Source code |
| plotQualByCycle | Source code |
| qQCReport | Source code |
| qcreport | Man page Source code |
| removeAdapter | Man page Source code |
| renamer | Man page Source code |
| sam2bam | Man page Source code |
| samToBed | Man page Source code |
| singleCall | Source code |
| snpanno | Man page Source code |
| truncStringToPlotWidth | Source code |
| tssQC | Man page Source code |
| unzipAndMerge | Man page Source code |
