Files in robertdouglasmorrison/DuffyNGS

Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

ConsensusProteinPileups.README.docx

DESCRIPTION

Makefile

NAMESPACE

R/.DS_Store

R/.Rapp.history

R/BAM.fileTools.R R/BAM.mpileupTools.R R/CP.R R/CR.R R/CRblast.R R/ChIP.peakPickTools.R R/DuffyNGS_Envir.R R/RIP.peakPickTools.R R/USR.R R/WB_Tools.R R/WIG_Tools.R R/alignToWig.R R/applyStageAdjustment.R R/bamChunkTools.R R/bamReadStats.R R/bowtie2Par.R R/bowtie2Version.R R/bowtiePar.R R/bowtieVersion.R R/buildAllAnnotationFiles.R R/buildBowtie1CommandLine.R R/buildBowtie2CommandLine.R R/buildBowtieCommandLine.R R/buildDetectibilityFiles.R R/buildRiboClearingFiles.R R/buildSpliceJunctionFiles.R R/calcAlignStats.R R/calcAlignSummary.R R/calcDEoneGeneFromTranscripts.R R/calcDiffExpressFromTranscripts.R R/calcStrandCC.R R/calcWIGmetrics.R R/calcWigChIPpeaks.R R/calcWigRIPpeaks.R R/calcWigTranscriptOneGene.R R/calcWigTranscriptome.R R/calculateRPKM.R R/calculateRPKMfold.R R/callBowtie.R R/callBowtie2.R R/checkDuffyPrograms.R R/cleanupFiles.R R/compressResults.R R/compressSpliceMaps.R R/countBAMreads.R R/countPolyBases.R R/cutadapt.R R/duffybamtools.R R/expressionUnits.R R/extractPipelineSummaryDetails.R R/extractRiboClearSummaryDetails.R R/fastCS2DNA.R R/fastSRO.R R/fastqReadStats.R R/fastqToBAM.R R/geneTableToHTML.R R/genericDiffExpression.R R/genericTranscriptome.R R/genomicConvert.R R/getBowtie2AlignMetrics.R R/getFastqFileNames.R R/loadDetectabilityToWB.R R/loadMultipleWIGs.R R/newWB.R R/pipe.AlignStats.R R/pipe.AlignToWig.R R/pipe.Alignment.R R/pipe.AlignmentPie.R R/pipe.AmpliconSequenceSurvey.R R/pipe.AssemblePseudoGenome.R R/pipe.BAMpileup.R R/pipe.BAMproteins.R R/pipe.BCR.TCR.Profile.R R/pipe.BarcodeSNPs.R R/pipe.BaselineAdjustTranscripts.R R/pipe.BuildCellTypeGeneAssociation.R R/pipe.BuildCellTypeGeneSetAssociation.R R/pipe.BuildCellTypeTargetMatrix.R R/pipe.CR_Investigate.R R/pipe.CellTypeProportions.R R/pipe.ChIPalignment.R R/pipe.ChIPpeaks.R R/pipe.ChIPseq.R R/pipe.ConsensusBaseCalls.R R/pipe.ConsensusProteinDifference.R R/pipe.ConsensusProteinExtraction.R R/pipe.ConsensusProteinPileups.R R/pipe.ConvertAllBAMs.R R/pipe.DESeq.R R/pipe.DNAalignment.R R/pipe.DNAseq.R R/pipe.DiffExpression.R R/pipe.EdgeR.R R/pipe.ExtractRiboClearedReadCounts.R R/pipe.ExtractWiggleDepths.R R/pipe.FastqReadStats.R R/pipe.FileCleanup.R R/pipe.FindDeletions.R R/pipe.GatherGeneAlignments.R R/pipe.GenomicAlign.R R/pipe.HLA.ConsensusProteins.R R/pipe.HLA.ContigProfile.R R/pipe.HLA.Expression.R R/pipe.HLAtyping.R R/pipe.IsoformExpression.R R/pipe.Kmerize.R R/pipe.LymphocyteProfile.R R/pipe.MARsurvey.R R/pipe.MatePairStatistics.R R/pipe.MetaResults.R R/pipe.NoHits_Investigate.R R/pipe.PlotGene.R R/pipe.PlotSNP.R R/pipe.PostAlignTasks.R R/pipe.PreAlignTasks.R R/pipe.QuickQC.R R/pipe.RIPalignment.R R/pipe.RIPpeaks.R R/pipe.RIPpeaksToAltGeneMap.R R/pipe.RIPseq.R R/pipe.RNAalignment.R R/pipe.RNAseq.R R/pipe.RankProduct.R R/pipe.ReadDepth.R R/pipe.RemoveDiscordantAlignFromNoHits.R R/pipe.RemoveReadsFromNoHits.R R/pipe.RenameSample.R R/pipe.RiboClear.R R/pipe.RnaEditingSearch.R R/pipe.RoundRobin.R R/pipe.SAM.R R/pipe.SNPmatrix.R R/pipe.ScaleFactorAdjustTranscripts.R R/pipe.SpadesContigs.R R/pipe.SpliceAlign.R R/pipe.SpliceCoverageAnalysis.R R/pipe.StrandVerify.R R/pipe.TargetSearch.R R/pipe.TranscriptCluster.R R/pipe.TranscriptToHTML.R R/pipe.Transcriptome.R R/pipe.USR.R R/pipe.UpdateWIGpathInfo.R R/pipe.VSAcoverage.R R/pipe.VargeneContigProfile.R R/pipe.VariantCalls.R R/pipe.VelvetContigs.R R/pipeline.R R/plotReadStats.R R/plotSNP.R R/plotWIG.R R/primerTailSearch.R R/proteinConstructPeptideMasking.R R/proteinConstructPeptidePileups.R R/proteinConstructPileupSummary.R R/readAlignmentFile.R R/readSense.R R/readTrimming.R R/riboConvert.R R/rosettaPvalue.R R/rosettaSigma.R R/roundRobinCompare.MatrixMethod.R R/roundRobinCompare.RatioMethod.R R/seqDataTools.R R/spadesTools.R R/spliceConvert.R R/spliceDetailSummary.R R/spliceJunctionLookup.R R/syntheticReads.R R/tpm.R R/velvetTools.R

README.DuffyNGS.Pipeline.docx

data/.DS_Store

data/Ag.by.Pb.detectable.WB.rda

data/Ag.by.Pf.detectable.WB.rda

data/Ag.by.Pv.detectable.WB.rda

data/Ag.by.Py17X.detectable.WB.rda

data/Ag.selfUnique.WB.rda

data/Agris.by.Pf.detectable.WB.rda

data/Agris.selfUnique.WB.rda

data/Anan.by.Pf.detectable.WB.rda

data/Anan.selfUnique.WB.rda

data/Asteph.by.Pf.detectable.WB.rda

data/Asteph.selfUnique.WB.rda

data/BCG.by.Hs.detectable.WB.rda

data/BCG.by.Mmus.detectable.WB.rda

data/BCG.selfUnique.WB.rda

data/Dmel.by.Pf.detectable.WB.rda

data/Dmel.selfUnique.WB.rda

data/Dr.by.MTb.detectable.WB.rda

data/Dr.selfUnique.WB.rda

data/Gsurd.by.Pb.detectable.WB.rda

data/Gsurd.by.Pf.detectable.WB.rda

data/Gsurd.selfUnique.WB.rda

data/Hs.by.BCG.detectable.WB.rda

data/Hs.by.KSHV.detectable.WB.rda

data/Hs.by.LmjF.detectable.WB.rda

data/Hs.by.MTb.detectable.WB.rda

data/Hs.by.Pf.detectable.WB.rda

data/Hs.by.Pv.detectable.WB.rda

data/Hs.selfUnique.WB.rda

data/KSHV.by.Hs.detectable.WB.rda

data/KSHV.selfUnique.WB.rda

data/Kphaf.by.Hs.detectable.WB.rda

data/Kphaf.selfUnique.WB.rda

data/LinJ.by.Hs.detectable.WB.rda

data/LinJ.selfUnique.WB.rda

data/Lmj.by.Hs.detectable.WB.rda

data/Lmj.selfUnique.WB.rda

data/LmjF.by.Hs.detectable.WB.rda

data/LmjF.selfUnique.WB.rda

data/MTb.by.Hs.detectable.WB.rda

data/MTb.by.Mmus.detectable.WB.rda

data/MTb.selfUnique.WB.rda

data/MTbHn878.by.Hs.detectable.WB.rda

data/MTbHn878.selfUnique.WB.rda

data/Mabsc.by.Hs.detectable.WB.rda

data/Mabsc.selfUnique.WB.rda

data/MacFas.by.Pco.detectable.WB.rda

data/MacFas.by.PcoAH.detectable.WB.rda

data/MacFas.by.PkH.detectable.WB.rda

data/MacFas.selfUnique.WB.rda

data/MacMu.by.Pco.detectable.WB.rda

data/MacMu.by.PcoAH.detectable.WB.rda

data/MacMu.by.Pk.detectable.WB.rda

data/MacMu.by.PkH.detectable.WB.rda

data/MacMu.selfUnique.WB.rda

data/Mchel.by.Hs.detectable.WB.rda

data/Mchel.selfUnique.WB.rda

data/Mmar.by.Dr.detectable.WB.rda

data/Mmar.selfUnique.WB.rda

data/Mmus.by.MTb.detectable.WB.rda

data/Mmus.by.Pb.detectable.WB.rda

data/Mmus.by.Pch.detectable.WB.rda

data/Mmus.by.Py17X.detectable.WB.rda

data/Mmus.by.Pym.detectable.WB.rda

data/Mmus.by.Styph.detectable.WB.rda

data/Mmus.selfUnique.WB.rda

data/Msmeg.by.Hs.detectable.WB.rda

data/Msmeg.selfUnique.WB.rda

data/Otsu.by.Hs.detectable.WB.rda

data/Otsu.by.Mmus.detectable.WB.rda

data/Otsu.selfUnique.WB.rda

data/Pb.by.Mmus.detectable.WB.rda

data/Pb.selfUnique.WB.rda

data/Pch.by.Gsurd.detectable.WB.rda

data/Pch.by.Mmus.detectable.WB.rda

data/Pch.selfUnique.WB.rda

data/Pco.by.Hs.detectable.WB.rda

data/Pco.by.MacFas.detectable.WB.rda

data/Pco.by.MacMu.detectable.WB.rda

data/Pco.selfUnique.WB.rda

data/PcoAH.by.Hs.detectable.WB.rda

data/PcoAH.by.MacFas.detectable.WB.rda

data/PcoAH.by.MacMu.detectable.WB.rda

data/PcoAH.selfUnique.WB.rda

data/Pcy.by.MacFas.detectable.WB.rda

data/Pcy.by.MacMu.detectable.WB.rda

data/Pcy.selfUnique.WB.rda

data/Pf.by.Ag.detectable.WB.rda

data/Pf.by.Hs.detectable.WB.rda

data/Pf.selfUnique.WB.rda

data/PfIT.by.Hs.detectable.WB.rda

data/PfIT.selfUnique.WB.rda

data/Pv.by.Ag.detectable.WB.rda

data/Pv.by.Hs.detectable.WB.rda

data/Pv.selfUnique.WB.rda

data/PvP01.by.Hs.detectable.WB.rda

data/PvP01.selfUnique.WB.rda

data/Py.by.Mmus.detectable.WB.rda

data/Py.selfUnique.WB.rda

data/Py17X.by.Ag.detectable.WB.rda

data/Py17X.by.Mmus.detectable.WB.rda

data/Py17X.selfUnique.WB.rda

data/Pym.by.Mmus.detectable.WB.rda

data/Pym.selfUnique.WB.rda

data/Styph.by.Mmus.detectable.WB.rda

data/Styph.selfUnique.WB.rda

data/Tbr.by.Hs.detectable.WB.rda

data/Tbr.selfUnique.WB.rda

data/Tbr427.by.Hs.detectable.WB.rda

data/Tbr427.selfUnique.WB.rda

html/pipe.ChIPpeaks.html

man/BAM_Files.Rd man/DuffyNGS.Rd man/DuffyNGS_Annotation.Rd man/DuffyNGS_Options.Rd man/MPU.callBases.Rd man/alignToWig.Rd man/bamAlign-class.Rd man/bamRange-class.Rd man/bamRange.Rd man/bamReadStats.Rd man/bamReader-class.Rd man/bamReader.Rd man/bowtie2Par.Rd man/buildAllAnnotationFiles.Rd man/buildBowtie2BuildCommandLine.Rd man/buildBowtie2CommandLine.Rd man/buildRiboClearingFiles.Rd man/buildSpliceJunctionFiles.Rd man/callBowtie2.Rd man/checkBowtie2Version.Rd man/compressSpliceMaps.Rd man/fastqToBAM.Rd man/getBowtie2AlignMetrics.Rd man/pipe.AlignStats.Rd man/pipe.AlignToWig.Rd man/pipe.Alignment.Rd man/pipe.BAMpileup.Rd man/pipe.ChIPpeaks.Rd man/pipe.DEtools.Rd man/pipe.DiffExpression.Rd man/pipe.ExtractPipelineSummaryDetails.Rd man/pipe.GenomicAlign.Rd man/pipe.MetaResults.Rd man/pipe.PlotGene.Rd man/pipe.PlotSNP.Rd man/pipe.PostAlignTasks.Rd man/pipe.PreAlignTasks.Rd man/pipe.QuickQC.Rd man/pipe.RIPpeaks.Rd man/pipe.RIPpeaksToAltGeneMap.Rd man/pipe.RNAseq.Rd man/pipe.RiboClear.Rd man/pipe.SpliceAlign.Rd man/pipe.TranscriptCluster.Rd man/pipe.TranscriptToHTML.Rd man/pipe.Transcriptome.Rd man/pipe.VariantCalls.Rd man/pipe.VariantSummary.Rd

src/.DS_Store

src/DuffyNGS.so

src/Makevars

src/align_list.h

src/duffybamtools.c

src/duffybamtools.c_old

src/duffybamtools.h

src/duffybamtools.h_old

src/duffybamtools.o

src/fastColorSpace2DNA.c

src/fastColorSpace2DNA.o

src/fastShortReadLocal.c

src/fastShortReadLocal.o

src/fastShortReadOverlap.c

src/fastShortReadOverlap.o

src/samtools-1.1_beta/bam.c

src/samtools-1.1_beta/bam.h

src/samtools-1.1_beta/bam.o

src/samtools-1.1_beta/bam_aux.c

src/samtools-1.1_beta/bam_aux.o

src/samtools-1.1_beta/bam_endian.h

src/samtools-1.1_beta/bam_import.c

src/samtools-1.1_beta/bam_import.o

src/samtools-1.1_beta/bam_index.c

src/samtools-1.1_beta/bam_index.o

src/samtools-1.1_beta/bam_sort.c

src/samtools-1.1_beta/bam_sort.o

src/samtools-1.1_beta/bgzf.c

src/samtools-1.1_beta/bgzf.o

src/samtools-1.1_beta/config.h

src/samtools-1.1_beta/faidx.c

src/samtools-1.1_beta/faidx.o

src/samtools-1.1_beta/htslib/bgzf.h

src/samtools-1.1_beta/htslib/faidx.h

src/samtools-1.1_beta/htslib/hfile.h

src/samtools-1.1_beta/htslib/hts.h

src/samtools-1.1_beta/htslib/hts_defs.h

src/samtools-1.1_beta/htslib/kfunc.h

src/samtools-1.1_beta/htslib/khash.h

src/samtools-1.1_beta/htslib/khash_str2int.h

src/samtools-1.1_beta/htslib/klist.h

src/samtools-1.1_beta/htslib/knetfile.h

src/samtools-1.1_beta/htslib/kseq.h

src/samtools-1.1_beta/htslib/ksort.h

src/samtools-1.1_beta/htslib/kstring.h

src/samtools-1.1_beta/htslib/sam.h

src/samtools-1.1_beta/htslib/synced_bcf_reader.h

src/samtools-1.1_beta/htslib/tbx.h

src/samtools-1.1_beta/htslib/vcf.h

src/samtools-1.1_beta/htslib/vcf_sweep.h

src/samtools-1.1_beta/htslib/vcfutils.h

src/samtools-1.1_beta/sam.c

src/samtools-1.1_beta/sam.h

src/samtools-1.1_beta/sam.o

src/samtools-1.1_beta/sam_header.c

src/samtools-1.1_beta/sam_header.h

src/samtools-1.1_beta/sam_header.o

src/samtools/.DS_Store

src/samtools/.bam_import.c.swp

src/samtools/LICENSE

src/samtools/bam.c

src/samtools/bam.h

src/samtools/bam.o

src/samtools/bam_aux.c

src/samtools/bam_aux.o

src/samtools/bam_endian.h

src/samtools/bam_import.c

src/samtools/bam_import.o

src/samtools/bam_index.c

src/samtools/bam_index.o

src/samtools/bam_sort.c

src/samtools/bam_sort.o

src/samtools/bgzf.c

src/samtools/bgzf.h

src/samtools/bgzf.o

src/samtools/faidx.c

src/samtools/faidx.h

src/samtools/faidx.o

src/samtools/khash.h

src/samtools/kseq.h

src/samtools/ksort.h

src/samtools/kstring.c

src/samtools/kstring.h

src/samtools/kstring.o

src/samtools/razf.c

src/samtools/razf.h

src/samtools/razf.o

src/samtools/sam.c

src/samtools/sam.h

src/samtools/sam.o

src/samtools/sam_header.c

src/samtools/sam_header.h

src/samtools/sam_header.o

robertdouglasmorrison/DuffyNGS documentation built on Sept. 1, 2024, 9:25 p.m.