wzthu/ATACpipe
An Easy-to-use Systematic pipeline for ATACseq data analysis

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Search the wzthu/ATACpipe package
Functions
343
Source code
52
Man pages
94
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wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis
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API

API for wzthu/ATACpipe
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
.f_dowle2 Man page
.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
.sc_renamer_call Source code
.type_chooser Source code
.write10xCounts Man page Source code
.write_hdf5 Source code
.write_sparse Source code
ATACProc-class Man page
AddMissingCells Man page Source code
ApplyMatrixByGroup Man page
AssignFragCellnames Man page Source code
BamToBed Man page
BedToBigWig Man page
BedUtils Man page
BinarizeCounts Man page Source code
Bowtie2Mapping Man page
Cells.Fragment Man page Source code
Cells<- Man page
Cells<-.Fragment Man page
ChrDivi_wrapper Source code
ChunkGRanges Man page Source code
CollapseToLongestTranscript Man page Source code
CountFragments Man page Source code
CreateFragmentObject Man page Source code
CutCountPre_wrapper Source code
CutSiteCountR Man page
CutSiteCount_wrapper Source code
CutSitePre Man page
Extend Man page
ExtractCell Man page Source code
ExtractFragments Man page Source code
FRiPQC Man page
FastQC Man page
FeatureMatrix Man page Source code
FilterCells Man page Source code
FindAdapter Man page
FragInRegions Man page
FragLenDistr Man page
Fragment Man page
Fragment-class Man page
Fragments Man page Source code
Fragments<- Man page
GRangesToString Man page Source code
GetCellsInRegion Man page Source code
GetFragmentData Man page Source code
GetGRangesFromEnsDb Man page Source code
GetReadsInRegion Man page
GetTSSPositions Man page Source code
LibComplexQC Man page
Links Man page Source code
Links<- Man page
MultiRegionCutMatrix Man page Source code
PartialMatrix Man page Source code
PeakCallingFseq Man page
PeakCallingMACS2 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
RegionMatrix Man page Source code
RegionStats Man page Source code
RemoveAdapter Man page
Renamer Man page
Rsortbam Man page
SCBowtie2Mapping Man page
SCCellFilter Man page
SCFindAdapter Man page
SCQC Man page
SCRemoveAdapter Man page
SCRenamer Man page
SCSamToBam Man page
SCUnzipAndMerge Man page
SamToBam Man page
SamToBed Man page
SetIfNull Man page Source code
SingleFeatureMatrix Man page Source code
SingleFileCutMatrix Man page
SingleRepReport Man page
SplitFragments Man page Source code
StringToGRanges Man page Source code
TSSQC Man page
TabixOutputToDataFrame Man page
UnzipAndMerge Man page
UpdatePath Man page Source code
ValidateCells Man page Source code
ValidateFragments Man page Source code
ValidateHash Man page Source code
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
atacPeakCallingMACS2 Man page
atacPeakCallingMACS2,ATACProc-method Man page
atacPeakComp Man page
atacPeakComp,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
atacSCBowtie2Mapping Man page
atacSCBowtie2Mapping,ATACProc-method Man page
atacSCCellFilter Man page
atacSCCellFilter,ATACProc-method Man page
atacSCFindAdapter Man page
atacSCFindAdapter,ATACProc-method Man page
atacSCQC Man page
atacSCQC,ATACProc-method Man page
atacSCRemoveAdapter Man page
atacSCRemoveAdapter,ATACProc-method Man page
atacSCRenamer Man page
atacSCRenamer,ATACProc-method Man page
atacSCSam2Bam Man page
atacSCSam2Bam,ATACProc-method Man page
atacSCUnzipAndMerge 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
atacscCellFilter Man page Source code
atacscQC Man page Source code
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
checkAndInstallGenomeSize 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
filterCells Source code
findAdapter Man page Source code
fragCreate Man page
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
groupCommand Source code
head.Fragment Man page Source code
isRemote Man page Source code
libComplexQC Man page Source code
lib_complex_qc Source code
listToFrame Source code Source code
mergeDF Man page
mergeFile Source code
mid_interval Source code
motifscan Man page Source code
motifscanpair Man page Source code
peakCalling Man page Source code
peakCallingMACS2 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
rename_fq Source code
renamer Man page Source code
sam2bam Man page Source code
samToBed Man page Source code
scBowtie2Mapping Man page Source code
scFindAdapter Man page Source code
scNucleosomeQC Man page
scPlotNucleosomeQC Man page
scPlotTssQC Man page
scRemoveAdapter Man page Source code
scRenamer Man page Source code
scSam2bam Man page Source code
scSingleCall Source code
scTssQC Man page
scUnzipAndMerge Man page Source code
sc_fastxrenamer Source code
singleCall Source code
snpanno Man page Source code
splitFragments Source code
testPeakCallingMACS2 Man page Source code
truncStringToPlotWidth Source code
tssQC Man page Source code
unzipAndMerge Man page Source code
validateCells Source code
wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.

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