Files in wzthu/ATACFlow
An Easy-to-use Systematic pipeline for ATACseq data analysis
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/ATACProc.R
R/BamToBed.R
R/BedToBigWig.R
R/BedUtils.R
R/ConfigVal.R
R/CppInterface.R
R/CutSiteCountR.R
R/CutSitePre.R
R/FRiPQC.R
R/FastQC.R
R/FindAdapter.R
R/FregLenDistribute.R
R/JavaExports.R
R/JavaInterface.R
R/LibComplexQC.R
R/Mapping.R
R/Methods.R
R/PeakCallingFseq.R
R/PeakCallingMACS2.R
R/PeakQC.R
R/RGo.R
R/RMotifScan.R
R/RMotifScanPair.R
R/RPeakAnno.R
R/RPeakComp.R
R/RSNPs.R
R/RcppExports.R
R/RemoveAdapter.R
R/Renamer.R
R/Rsortbam.R
R/SamToBam.R
R/SamToBed.R
R/SingleRepReport.R
R/TSSQC.R
R/UnzipAndMerge.R
R/fragmentObject.R
R/generics.R
R/onLoad.R
R/sc10XMatrix.R
R/scCellFilter.R
R/scFindAdapter.R
R/scMapping.R
R/scQC.R
R/scRemoveAdapter.R
R/scRenamer.R
R/scSamToBam.R
R/scUnzipAndMerge.R
R/scUtilities.R
R/utilities.R
inst/CITATION
inst/NEWS
inst/extdata/CustomizedMotif.txt
inst/extdata/Example.sam.bz2
inst/extdata/Example_peak1.bed.bz2
inst/extdata/Example_peak2.bed.bz2
inst/extdata/MotifPFM.rds
inst/extdata/Rep_Report.Rmd
inst/extdata/Rep_Report2.Rmd
inst/extdata/Rep_Report_Index.Rmd
inst/extdata/Report.Rmd
inst/extdata/Report2.Rmd
inst/extdata/Report_Index.Rmd
inst/extdata/basicReport.Rmd
inst/extdata/bt2/reads/reads_1.fastq
inst/extdata/bt2/reads/reads_2.fastq
inst/extdata/bt2/refs/lambda_virus.fa
inst/extdata/chr20.50000.bed.bz2
inst/extdata/chr20_1.1.fq.gz
inst/extdata/chr20_1.2.fq.bz2
inst/extdata/chr20_2.1.fq.gz
inst/extdata/chr20_2.2.fq.bz2
inst/extdata/chr20_sample_peak.bed.bz2
inst/extdata/hg19.blacklist.bed
inst/extdata/scATAC/cell_name.txt
inst/extdata/scATAC/fragments.tsv.gz
inst/extdata/scATAC/fragments.tsv.gz.tbi
inst/extdata/scATAC/peaks.rds
inst/extdata/snp_info
inst/extdata/uzmg/m1/reads_1.fastq.1.bz2
inst/extdata/uzmg/m1/reads_1.fastq.2
inst/extdata/uzmg/m1/reads_1.fastq.gz
inst/extdata/uzmg/m2/reads_2.fastq.1.bz2
inst/extdata/uzmg/m2/reads_2.fastq.2
inst/extdata/uzmg/m2/reads_2.fastq.gz
inst/java/commons-cli-1.1.jar
inst/java/fseq.jar
man/ATACProc-class.Rd
man/AddMissingCells.Rd
man/ApplyMatrixByGroup.Rd
man/AssignFragCellnames.Rd
man/BamToBed.Rd
man/BedToBigWig.Rd
man/BedUtils.Rd
man/BinarizeCounts.Rd
man/Bowtie2Mapping.Rd
man/Cells-set-.Fragment.Rd
man/Cells-set.Rd
man/ChunkGRanges.Rd
man/CollapseToLongestTranscript.Rd
man/CountFragments.Rd
man/CreateFragmentObject.Rd
man/CutSiteCountR.Rd
man/CutSitePre.Rd
man/Extend.Rd
man/ExtractCell.Rd
man/ExtractFragments.Rd
man/FRiPQC.Rd
man/FastQC.Rd
man/FeatureMatrix.Rd
man/FilterCells.Rd
man/FindAdapter.Rd
man/FragInRegions.Rd
man/FragLenDistr.Rd
man/Fragment-class.Rd
man/Fragments-set.Rd
man/Fragments.Rd
man/GRangesToString.Rd
man/GetCellsInRegion.Rd
man/GetFragmentData.Rd
man/GetGRangesFromEnsDb.Rd
man/GetReadsInRegion.Rd
man/GetTSSPositions.Rd
man/LibComplexQC.Rd
man/Links-set.Rd
man/Links.Rd
man/MultiRegionCutMatrix.Rd
man/PartialMatrix.Rd
man/PeakCallingFseq.Rd
man/PeakCallingMACS2.Rd
man/PeakQC.Rd
man/RGo.Rd
man/RMotifScan.Rd
man/RMotifScanPair.Rd
man/RPeakAnno.Rd
man/RPeakComp.Rd
man/RSNPs.Rd
man/RegionMatrix.Rd
man/RegionStats.Rd
man/RemoveAdapter.Rd
man/Renamer.Rd
man/Returns.Rd
man/Rsortbam.Rd
man/SCBowtie2Mapping.Rd
man/SCCellFilter.Rd
man/SCFindAdapter.Rd
man/SCQC.Rd
man/SCRemoveAdapter.Rd
man/SCRenamer.Rd
man/SCSamToBam.Rd
man/SCUnzipAndMerge.Rd
man/SamToBam.Rd
man/SamToBed.Rd
man/SetIfNull.Rd
man/SingleFeatureMatrix.Rd
man/SingleFileCutMatrix.Rd
man/SingleRepReport.Rd
man/SplitFragments.Rd
man/StringToGRanges.Rd
man/TSSQC.Rd
man/TabixOutputToDataFrame.Rd
man/This.Rd
man/UnzipAndMerge.Rd
man/UpdatePath.Rd
man/ValidateCells.Rd
man/ValidateFragments.Rd
man/ValidateHash.Rd
man/atacPipe2.Rd
man/atacRepsPipe.Rd
man/atacRepsPipe2.Rd
man/dot-f_dowle2.Rd
man/dot-write10xCounts.Rd
man/esATAC-package.Rd
man/fragCreate.Rd
man/getMotifInfo.Rd
man/isRemote.Rd
man/mergeDF.Rd
man/scNucleosomeQC.Rd
man/scPlotNucleosomeQC.Rd
man/scPlotTssQC.Rd
man/scTssQC.Rd
src/BedLine.cpp
src/BedLine.h
src/BedUtils.cpp
src/BedUtils.h
src/ChrDivi.cpp
src/ChrDivi.h
src/CutCountPre.cpp
src/CutCountPre.h
src/CutSiteCount.cpp
src/CutSiteCount.h
src/LibComplexQC.cpp
src/LibComplexQC.h
src/Makevars
src/Makevars.win
src/RcoutRcerr.h
src/RcppExports.cpp
src/SortBed.cpp
src/SortBed.h
src/filter.cpp
src/group.cpp
src/group.h
src/rcpp_wrapper.cpp
src/renamer.cpp
src/renamer.h
src/sam2bed.cc
src/sam2bed.h
src/sc_renamer.cpp
src/sc_renamer.h
src/split.cpp
src/validate.cpp
tests/testthat.R
tests/testthat/test-basicopr.R
vignettes/esATAC-Introduction.R
vignettes/esATAC-Introduction.Rmd
vignettes/whole.png
