Files in KasperThystrup/circulaR

Characterization of circRNAs from Total RNA-seq data

LICENSE.md R/S4_classes.R R/S4_generics.R R/S4_methods.R R/check_mate.r R/chimeric_data_manipulation.r R/circRNA_annotation.r R/circulaR.r R/data_io.r R/helper_functions.r R/plot_functions.r R/startUp.r R/statistics.R R/testS4.R README.Rmd README.md man/BSJTrack.Rd man/SJTrack.Rd man/STARlogParser.Rd man/addFilter.Rd man/addKnownJunctions.Rd man/addLinCounts.Rd man/adjustAlignment.Rd man/alignmentStats.Rd man/annotateByOverlap.Rd man/bam.file-set.Rd man/bam.file.Rd man/bsReadCoverage.Rd man/bsid2bed.Rd man/bsid2gr.Rd man/bsid2junc.Rd man/bsj.counts-set.Rd man/bsj.counts.Rd man/bsj.reads-set.Rd man/bsj.reads.Rd man/bsjExonStats.Rd man/bsjStats.Rd man/c2l.ratio.Rd man/calcCoverage.Rd man/categorizeBSJ.Rd man/checkChimFile.Rd man/checkInputFiles.Rd man/checkPEReads.Rd man/checkPEReads_old.Rd man/checkVariables.Rd man/chim.file-set.Rd man/chim.file.Rd man/cigar2covr.Rd man/circExperiment-class.Rd man/circSample.Rd man/circulaR.Rd man/compareToKnownJunctions.Rd man/constructBsId.Rd man/constructSJDB.Rd man/count.file-set.Rd man/count.file.Rd man/countSumChimFile.Rd man/determineAmbiguousHits.Rd man/exp.mat.Rd man/findNearest.Rd man/firstread.firststrand-set.Rd man/firstread.firststrand.Rd man/gb-set.Rd man/gb.Rd man/generateJunctionMotifs.Rd man/getCandidateBackspliceSites.Rd man/getKnownJunctions.Rd man/guessPE.Rd man/indexJunctions.Rd man/inferExons.Rd man/is.empty.Rd man/junctionMotif.Rd man/junctionsToGRanges.Rd man/knownJunctionInRepeatRegion.Rd man/knownJunctionSites.Rd man/label-set.Rd man/label.Rd man/locateSamples.Rd man/log.file-set.Rd man/log.file.Rd man/lsj.counts-set.Rd man/lsj.counts.Rd man/name-set.Rd man/name.Rd man/paired.end-set.Rd man/paired.end.Rd man/parseCIGAR.Rd man/parseDataDir.Rd man/path.Rd man/plotAll.Rd man/plotBSJ.Rd man/plotBSJrepeats.Rd man/plotCoverage.Rd man/plotSJ.Rd man/plotTxModels.Rd man/plotTxModelsOLD.Rd man/pruneChromosomes.Rd man/readBSJdata.Rd man/readChimFile.Rd man/readLSJdata.Rd man/rescueAmbiguous.Rd man/resolveReads.Rd man/sample.id-set.Rd man/sample.id.Rd man/samples-circExperiment-method.Rd man/samples-set.Rd man/shiftAlignment.Rd man/sj.file-set.Rd man/sj.file.Rd man/summarizeBSJreads.Rd man/swapStrands.Rd man/vizJunctions.Rd man/wrapperFunction.Rd tests/testthat.R tests/testthat/test_S4_functions.r tests/testthat/test_annotation.r tests/testthat/test_checkmate.r tests/testthat/test_chimeric.r tests/testthat/test_dataio.R tests/testthat/test_helper.r