Files in UofABioinformaticsHub/rnaCleanR
Calculate strandness information of a bam file
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/aaa.R
R/calculateStrandCoverage.R
R/calculateStrandNbReads.R
R/checkPairedEnd.R
R/concatenateAlignments.R
R/filterDNA.R
R/getStrandFromBamFile.R
R/getStrandFromReadInfo.R
R/getWinInSequence.R
R/getWinOverlapEachIRange.R
R/getWinOverlapEachReadFragment.R
R/getWinOverlapGRanges.R
R/intersectWithFeature.R
R/keptProbaWin.R
R/keptReadFragment.R
R/plotHist.R
R/plotWin.R
R/sequenceInfoInPartition.R
R/summarizeHist.R
README.Rmd
README.md
README_files/figure-markdown_github/plotHist-1.png
README_files/figure-markdown_github/plotHistAfterFilter-1.png
README_files/figure-markdown_github/plotWin-1.png
inst/extdata/paired.bam
inst/extdata/paired.bam.bai
inst/extdata/s1.sorted.bam
inst/extdata/s1.sorted.bam.bai
inst/extdata/s2.sorted.bam
inst/extdata/s2.sorted.bam.bai
man/checkPairedEnd.Rd
man/dot-calculateStrandCoverage.Rd
man/dot-calculateStrandNbReads.Rd
man/dot-concatenateAlignments.Rd
man/dot-getWinInSequence.Rd
man/dot-keptProbaWin.Rd
man/dot-keptReadFragment.Rd
man/dot-sequenceInfoInPartition.Rd
man/dot-summarizeHist.Rd
man/filterDNA.Rd
man/getStrandFromBamFile.Rd
man/getStrandFromReadInfo.Rd
man/getWinOverlapEachIRange.Rd
man/getWinOverlapEachReadFragment.Rd
man/getWinOverlapGRanges.Rd
man/intersectWithFeature.Rd
man/plotHist.Rd
man/plotWin.Rd
man/strandCheckR-package.Rd
paper/Rplot1.png
paper/Rplot2.png
paper/Rplot3.png
paper/paper.bib
paper/paper.md
tests/testthat.R
tests/testthat/test_calculateStrandCoverage.R
tests/testthat/test_calculateStrandNbReads.R
tests/testthat/test_checkPairedEnd.R
tests/testthat/test_concatenateAlignments.R
tests/testthat/test_filterDNA.R
tests/testthat/test_getStrandFromBamFile.R
tests/testthat/test_getStrandFromReadInfo.R
tests/testthat/test_getWinIdFromIRanges.R
tests/testthat/test_getWinIdOverlapAlignments.R
tests/testthat/test_getWinInSequence.R
tests/testthat/test_keptProbaWin.R
tests/testthat/test_keptReadFragment.R
tests/testthat/test_plotHist.R
tests/testthat/test_plotWin.R
tests/testthat/test_sequenceInfoInPartition.R
tests/testthat/test_summarizeHist.R
vignettes/strandCheckR.Rmd
