Files in wzthu/esATAC
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
wzthu/esATAC documentation built on Aug. 12, 2022, 7:41 a.m.