Files in PietaSchofield/plibb

Pieta Schofield's repository of former useful R functions

R/CitePres.R R/DSFromFC.R R/addCite.R R/alignBWA.R R/alignStar.R R/alignSubjunc.R R/alignSubread.R R/applyQDNAFilter.R R/autoCommit.R R/bamToBed.R R/base2dec.R R/bigcor.R R/bigcor_spiess.R R/buildAll.R R/cnvAnnoGenes.R R/cnvAnnoSegs.R R/cnvCalcLogRatio.R R/cnvCopyNumber.R R/cnvGIindex.R R/cnvSegment.R R/codeHook.R R/collateRPG.R R/custHMMseqment.R R/data.R R/dedupCNV.R R/delWeek.R R/edt.R R/evalCluster.R R/evalSignatureSurv.R R/factorise.R R/genBibtex.R R/genCNValignmentStats.R R/genCNVmapGC.R R/genCNVwigs.R R/genCovTracks.R R/genPBSHead.R R/genSGEHead.R R/genSRstats.R R/genSlurmHead.R R/getFiles.R R/getProject.R R/getQC.R R/getSpikeInNorm.R R/getWeek.R R/go.R R/hmAnalysis.R R/knithook_plot.R R/lck.R R/listcitekeys.R R/loadSubreadOutput.R R/logRun.R R/logTime.R R/mergeBAMS.R R/multiplot.R R/myKMplot.R R/newFile.R R/newNote.R R/newProject.R R/plib.R R/plotCNV.R R/plotSubTree.R R/pubGoD.R R/publish.R R/qstat.R R/rb.R R/rcmd.R R/rcur.R R/readDREME.R R/readENCODE.R R/readFC.R R/readGMT.R R/readMEME.R R/readPrism.R R/readTRANSFAC.R R/retGenBank.R R/rlsFiles.R R/rsh.R R/runCPH.R R/runFC.R R/runFastQC.R R/runHMMcopy.R R/runJAFFA.R R/runMACS2.R R/runQSTrim.R R/runQualimap.R R/runRScript.R R/runSICER.R R/runScript.R R/runStarAlign.R R/sortBAM.R R/splitBam.R R/splitStrandedBam.R R/ssBAMtoBWs.R R/strandedBamImport.R R/stripPlurals.R R/subFastQC.R R/subJob.R R/sumCNValignStats.R R/sumForPlot.R R/summariseQualiMap.R R/summariseSTAR.R R/summariseSubread.R R/survAnal.R R/survAnal2.R R/survClust.R R/survClustAnal.R R/survFit.R R/survFit2.R R/survFit3.R R/tabixFile.R R/view.R R/wigToBigWig.R README.md man/CitePres.Rd man/DSFromFC.Rd man/addCite.Rd man/alignBWA.Rd man/alignStar.Rd man/alignSubjunc.Rd man/alignSubread.Rd man/anscore.Rd man/applyQDNAFilter.Rd man/autoCommit.Rd man/bamToBed.Rd man/base2dec.Rd man/bigcor.Rd man/buildAll.Rd man/cnvAnnoGenes.Rd man/cnvAnnoSegs.Rd man/cnvCopyNumber.Rd man/cnvGIindex.Rd man/cnvLogRatio.Rd man/cnvSegment.Rd man/codeHook.Rd man/collateRPG.Rd man/custHMMsegment.Rd man/dedupCNV.Rd man/delWeek.Rd man/edt.Rd man/evalCluster2.Rd man/evalSigSurv.Rd man/factorise.Rd man/filter150kb.Rd man/genBibtex.Rd man/genCNValignmentStats.Rd man/genCNVmapGC.Rd man/genCNVwigs.Rd man/genCovTracks.Rd man/genPBSHead.Rd man/genSGEHead.Rd man/genSRstats.Rd man/genSlurmHead.Rd man/getFiles.Rd man/getProject.Rd man/getQC.Rd man/getSpikeInNorm.Rd man/getWeek.Rd man/go.Rd man/hmAnalysis.Rd man/knithook_plot.Rd man/lck.Rd man/loadSubreadOutput.Rd man/logRun.Rd man/logTime.Rd man/macOpen.Rd man/mergeBAMS.Rd man/multiplot.Rd man/newFile.Rd man/newNote.Rd man/newProject.Rd man/plib.Rd man/plotCNV.Rd man/plotKM.Rd man/plotSubTree.Rd man/pubGoD.Rd man/publish.Rd man/qstat.Rd man/rb.Rd man/rc.Rd man/rcmd.Rd man/readDREME.Rd man/readENCODE.Rd man/readFC.Rd man/readGMT.Rd man/readMEME.Rd man/readPrism.Rd man/readTRANSFACT.Rd man/retGenBank.Rd man/rlsFiles.Rd man/rsh.Rd man/runCPH.Rd man/runFC.Rd man/runFastQC.Rd man/runHMMcopy.Rd man/runJAFFA.Rd man/runMACS2.Rd man/runQSTrim.Rd man/runQualimap.Rd man/runRScript.Rd man/runSICER.Rd man/runScript.Rd man/runStarAlign.Rd man/sortBAM.Rd man/splitBAMS.Rd man/splitStrandedBAM.Rd man/ssBAMtoBWs.Rd man/sswigToBigWig.Rd man/strandedBamImport.Rd man/stripPlurals.Rd man/subFastQC.Rd man/subJob.Rd man/sumCNValignStats.Rd man/sumForPlot.Rd man/summariseQualimap.Rd man/summariseSTAR.Rd man/summariseSubread.Rd man/survAnal.Rd man/survAnal2.Rd man/survClust.Rd man/survClustAnal.Rd man/survFit.Rd man/survFit2.Rd man/survFit3.Rd man/tabixFile.Rd