Files in esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysis

LICENSE
DESCRIPTION
.BBSoptions
NAMESPACE
inst/NEWS
inst/CITATION
inst/doc/esATAC-Introduction.Rmd inst/doc/esATAC-Introduction.R
inst/doc/esATAC-Introduction.html
inst/java/fseq.jar
inst/java/commons-cli-1.1.jar
inst/extdata/Rep_Report.Rmd
inst/extdata/hg19.blacklist.bed
inst/extdata/snp_info
inst/extdata/CustomizedMotif.txt
inst/extdata/basicReport.Rmd
inst/extdata/Example.sam.bz2
inst/extdata/chr20_2.1.fq.gz
inst/extdata/Report_Index.Rmd
inst/extdata/Example_peak2.bed.bz2
inst/extdata/Rep_Report2.Rmd
inst/extdata/MotifPFM.rds
inst/extdata/Report.Rmd
inst/extdata/chr20_1.1.fq.gz
inst/extdata/chr20_2.2.fq.bz2
inst/extdata/Report2.Rmd
inst/extdata/chr20_1.2.fq.bz2
inst/extdata/Example_peak1.bed.bz2
inst/extdata/Rep_Report_Index.Rmd
inst/extdata/chr20.50000.bed.bz2
inst/extdata/chr20_sample_peak.bed.bz2
inst/extdata/uzmg/m1/reads_1.fastq.2
inst/extdata/uzmg/m1/reads_1.fastq.gz
inst/extdata/uzmg/m1/reads_1.fastq.1.bz2
inst/extdata/uzmg/m2/reads_2.fastq.1.bz2
inst/extdata/uzmg/m2/reads_2.fastq.gz
inst/extdata/uzmg/m2/reads_2.fastq.2
inst/extdata/bt2/reads/reads_2.fastq
inst/extdata/bt2/reads/reads_1.fastq
inst/extdata/bt2/refs/lambda_virus.fa
vignettes/wave.png
vignettes/esATAC-Introduction.Rmd
vignettes/CTCF_footprint.png
vignettes/fregLenDistr.png
R/SamToBam.R R/RPeakComp.R R/JavaExports.R R/RSNPs.R R/RMotifScan.R R/BedUtils.R R/RemoveAdapter.R R/RPeakAnno.R R/Renamer.R R/TSSQC.R R/RcppExports.R R/BedToBigWig.R R/utilities.R R/RMotifScanPair.R R/CppInterface.R R/FregLenDistribute.R R/FastQC.R R/BaseProc.R R/ConfigVal.R R/PeakCallingFseq.R R/UnzipAndMerge.R R/LibComplexQC.R R/Mapping.R R/CutSiteCountR.R R/FRiPQC.R R/onLoad.R R/SamToBed.R R/RGo.R R/Methods.R R/PeakQC.R R/JavaInterface.R R/Rsortbam.R R/GraphMng.R R/BamToBed.R R/CutSitePre.R
src/SortBed.h
src/LibComplexQC.h
src/SortBed.cpp
src/sam2bed.h
src/Makevars.win
src/renamer.h
src/BedUtils.cpp
src/BedLine.h
src/rcpp_wrapper.cpp
src/LibComplexQC.cpp
src/CutCountPre.h
src/RcppExports.cpp
src/ChrDivi.h
src/sam2bed.cc
src/RcoutRcerr.h
src/Makevars
src/CutCountPre.cpp
src/BedUtils.h
src/ChrDivi.cpp
src/CutSiteCount.h
src/renamer.cpp
src/CutSiteCount.cpp
src/BedLine.cpp
man/ATACProc-class.Rd man/LibComplexQC.Rd man/atacRepsPipe.Rd man/RMotifScan.Rd man/TSSQC.Rd man/CutSitePre.Rd man/esATAC-package.Rd man/RPeakComp.Rd man/getMotifInfo.Rd man/BedToBigWig.Rd man/SamToBed.Rd man/Rsortbam.Rd man/FragLenDistr.Rd man/RGo.Rd man/PeakQC.Rd man/UnzipAndMerge.Rd man/BedUtils.Rd man/atacPipe2.Rd man/RMotifScanPair.Rd man/BamToBed.Rd man/CutSiteCountR.Rd man/FripQC.Rd man/Renamer.Rd man/RSNPs.Rd man/PeakCallingFseq.Rd man/configureValue.Rd man/RemoveAdapter.Rd man/Bowtie2Mapping.Rd man/FastQC.Rd man/RPeakAnno.Rd man/atacRepsPipe2.Rd man/SamToBam.Rd
build/vignette.rds
tests/testthat.R tests/testthat/test-sambamopr.R tests/testthat/test-basicopr.R tests/testthat/test-premapping.R tests/testthat/test-qcopr.R
esATAC documentation built on Oct. 6, 2018, 6 p.m.