Files in HenrikBengtsson/aroma.seq

High-Throughput Sequence Analysis using the Aroma Framework

R/000.R R/999.AromaSeq.R R/999.NonDocumentedObjects.R R/999.package.R R/AbstractAlignment.R R/AbstractIndexFile.R R/AbstractIndexSet.R R/AromaPathnameInterface.R R/AromaSeqTransform.R R/AromaUgpFile.XTRAS.R R/AromaUnitNucleotideCountsFile.R R/BamDataFile.R R/BamDataSet.R R/BamDownsampler.R R/BamIndexDataFile.R R/BamMerger.R R/BinnedGcNormalization.R R/Bowtie2Alignment.R R/Bowtie2IndexFile.R R/Bowtie2IndexSet.R R/BwaAlignment.R R/BwaIndexFile.R R/BwaIndexSet.R R/CnvKitCopyNumberRatioFile.R R/FastQCDataFile.R R/FastQCDataFileSet.R R/FastQCReporter.R R/FastaReferenceFile.R R/FastaReferenceIndexFile.R R/FastaReferenceSet.R R/FastaReferenceSet.writeFastaReferenceFile.R R/FastqDataFile,REPORT.R R/FastqDataFile.R R/FastqDataSet.R R/FastqDownsampler.R R/FastqQualityReport.R R/FileGroupsInterface.R R/GatkAlleleCounting.R R/GcBaseFile.R R/GenericDataFile.MEMOIZATION.R R/GtfDataFile.R R/HTSeqCountDataFile.R R/HTSeqCountDataSet.R R/HTSeqCounting.R R/IlluminaFastqDataFile.R R/IlluminaFastqDataSet.R R/MPileupFile.R R/MaskedDNAString.EXTS.R R/PairedEndFastqDataSet.R R/PicardDuplicateRemoval.R R/QDNAseqEstimation.R R/SamDataFile.R R/SamDataSet.R R/SamReadGroup.R R/SamTransform.R R/SequenceContigsInterface.R R/SeqzFile.R R/SraDataFile.R R/SraDataSet.R R/TopHat2Alignment.R R/TotalCnBinnedCounting.R R/agsub.R R/asserts.R R/bowtie2.R R/bowtie2Build.R R/bowtie2IndexPrefix.R R/buildTopHat2TranscriptomeIndexSet.R R/bwaAln.R R/bwaIndex.R R/bwaIndexPrefix.R R/bwaSampe.R R/bwaSamse.R R/convertToBam.R R/convertToSam.R R/countNucleotides.R R/createIndexPrefix.R R/cuffdiff.R R/cufflinks.R R/directoryStructure.R R/doBWA.R R/doBowtie2.R R/doDownsample.R R/doHTSeqCount.R R/doQDNAseq.R R/doTopHat2.R R/fastQC.R R/fastqDump.R R/findBWA.R R/findBowtie2.R R/findCNVkit.R R/findCache.R R/findCmd.R R/findCmdv.R R/findExternal.R R/findFastQC.R R/findFastqDump.R R/findFilesTodo.R R/findGATK.R R/findHTSeq.R R/findJava.R R/findPerl.R R/findPicard.R R/findPython.R R/findRspReportTemplate.R R/findSamtools.R R/findSraToolkit.R R/findTopHat.R R/gatk.R R/getOutputDataSet.R R/htseqCount.R R/isCompatibleWith.R R/mpileup.R R/normalizeGCContent.R R/onExit.R R/optionsList2String.R R/pi3.R R/picardValidateSamFile.R R/pileup2seqz.R R/readSeqFile.R R/samtoolsFaidx.R R/samtoolsMpileup.R R/samtoolsSort.R R/samtoolsView.R R/segmentByPairedPSCBS.SeqzFileSet.R R/setupExampleData.R R/sortByName.R R/sortByPosition.R R/systemBWA.R R/systemBowtie2.R R/systemBowtie2Build.R R/systemCuffdiff.R R/systemCufflinks.R R/systemFastQC.R R/systemFastqDump.R R/systemGATK.R R/systemGenericCmd.R R/systemHTSeqCount.R R/systemJava.R R/systemPicard.R R/systemSamtools.R R/systemSraToolkit.R R/systemTopHat.R R/systemTopHatBuild.R R/tophat.R R/typeOfSeqNamesOrdering.R R/utils.R R/zzz.R README.md inst/BatchJobs,config/__BatchJobs,interactive.BatchJobs,interactive.R inst/BatchJobs,config/__BatchJobs,interactive.BatchJobs,multicore.R inst/BatchJobs,config/__BatchJobs,interactive.BatchJobs,torque.R inst/buildScripts/chipTypes/GenericHuman/GenericHuman,SNPs,UGP.R inst/buildScripts/organisms/Mus_musculus/01.mm10,mergeFASTA.R inst/buildScripts/organisms/Mus_musculus/01.mm9,mergeFASTA.R inst/buildScripts/organisms/Saccharomyces_cerevisiae/01.mergeFASTA.R inst/buildScripts/organisms/Saccharomyces_cerevisiae/02.FASTA-to-Bowtie2Index.R inst/testScripts/AndersEtAl/2013/doCounts.R inst/testScripts/AndersEtAl/2013/doEdgeR.R inst/testScripts/AndersEtAl/2013/doSam.R inst/testScripts/AndersEtAl/2013/doTopHat.R inst/testScripts/AndersEtAl/2013/download.R inst/testScripts/AndersEtAl/2013/main.R inst/testScripts/AndersEtAl/2013/preProcess.R inst/testScripts/AndersEtAl/runAnders.R inst/testScripts/ExomeSeq/proto.R inst/testScripts/R/downloadUtils.R inst/testScripts/R/installUtils.R inst/testScripts/R/launchUtils.R inst/testScripts/RnaSeqProto/rnaSeqScript.R inst/testScripts/RnaSeqProto/yeast/checkConfig.R inst/testScripts/RnaSeqProto/yeast/protoYeast.R inst/testScripts/RnaSeqProto/yeast/setupConfig.R inst/testScripts/RnaSeqProto/yeast/setupDirs.R inst/testScripts/RnaSeqTest/testRnaSeq.R inst/testScripts/RnaSeqTest/testTA.R inst/testScripts/bowtie2/20120831a-bowtie2,lambda_virus,paired-end,system-level.R inst/testScripts/bowtie2/20120831a-bowtie2,lambda_virus,single-end,system-level.R inst/testScripts/bowtie2/testSystemBowtie2Build.R inst/testScripts/bwa/01a.downloadAnnotationData.R inst/testScripts/bwa/01b.downloadRawData.R inst/testScripts/bwa/11.bwa,index,level1.R inst/testScripts/bwa/11.bwa,index,level2.R inst/testScripts/bwa/11.bwa,index,level3.R inst/testScripts/bwa/21.bwa,align,single-end,level1.R inst/testScripts/bwa/21.bwa,align,single-end,level2.R inst/testScripts/bwa/21.bwa,align,single-end,level3.R inst/testScripts/complete/LambdaVirusExample/01a.downloadAnnotationData.R inst/testScripts/complete/LambdaVirusExample/01b.downloadRawData.R inst/testScripts/complete/LambdaVirusExample/01c.installPackages.R inst/testScripts/complete/LambdaVirusExample/21.BwaAlignment,PicardDuplicateRemoval.R inst/testScripts/complete/LambdaVirusExample/21.BwaAlignment.R inst/testScripts/complete/LambdaVirusExample/31.Bowtie2Alignment,PicardDuplicateRemoval.R inst/testScripts/complete/LambdaVirusExample/31.Bowtie2Alignment.R inst/testScripts/complete/LambdaVirusExample/41.FastqDataSet,QC.R inst/testScripts/complete/TrapnellC_etal_2012/05.downloadData.R inst/testScripts/complete/TrapnellC_etal_2012/11.doTopHat2.R inst/testScripts/complete/VUMC/01a.downloadAnnotationData.R inst/testScripts/complete/VUMC/21.BwaAlignment.R inst/testScripts/complete/VUMC/21.IlluminaFastqDataSet.R inst/testScripts/complete/VUMC/21.TotalCNs.R inst/testScripts/complete/VUMC/31.BamDataSet,TotalCNs.R inst/testScripts/complete/VUMC/41.TotalCnBinnedCounting.R inst/testScripts/complete/VUMC/51.GcNormalization.R inst/testScripts/complete/VUMC/61.AlleleCounts.R inst/testScripts/complete/VUMC/71.doQDNASeq.R inst/testScripts/complete/VUMC/91.FASTQ-to-CBS.R inst/testScripts/complete/VUMC/92.PSCN.R inst/testScripts/complete/hg19/01a.downloadAnnotationData.R inst/testScripts/complete/hg19/01c.installPackages.R inst/testScripts/complete/hg19/21.FastaReferenceFile,BWA.R inst/testScripts/complete/hg19/21.FastaReferenceFile,Bowtie2.R inst/testScripts/complete/hg19/31.BinnedACGT,BioC.R inst/testScripts/cufflinks/testCufflinks.R inst/testScripts/setup/00a.setup.R inst/testScripts/setup/01a.downloadAllAnnotationData.R inst/testScripts/setup/01b.downloadAllRawDataSet.R inst/testScripts/setup/01c.installAllPackages.R inst/testScripts/setup/99a.cleanupRootDirectories.R inst/testScripts/tophat/testSystemTopHatBuild.R man/AbstractAlignment.Rd man/AbstractIndexFile.Rd man/AbstractIndexSet.Rd man/AromaSeq.Rd man/AromaSeqTransform.Rd man/BamDataFile.Rd man/BamDataSet.Rd man/BamDownsampler.Rd man/BamIndexDataFile.Rd man/BamMerger.Rd man/BinnedGcNormalization.Rd man/Bowtie2Alignment.Rd man/Bowtie2IndexFile.Rd man/Bowtie2IndexSet.Rd man/BwaAlignment.Rd man/BwaIndexFile.Rd man/BwaIndexSet.Rd man/FastQCDataFile.Rd man/FastQCDataFileSet.Rd man/FastQCReporter.Rd man/FastaReferenceFile.Rd man/FastaReferenceIndexFile.Rd man/FastaReferenceSet.Rd man/FastqDataFile.Rd man/FastqDataSet.Rd man/FastqDownsampler.Rd man/GtfDataFile.Rd man/HTSeqCountDataFile.Rd man/HTSeqCountDataSet.Rd man/HTSeqCounting.Rd man/IlluminaFastqDataFile.Rd man/IlluminaFastqDataSet.Rd man/Non-documented_objects.Rd man/PairedEndFastqDataSet.Rd man/PicardDuplicateRemoval.Rd man/QDNAseqEstimation.Rd man/SamDataFile.Rd man/SamDataSet.Rd man/SamReadGroup.Rd man/SamTransform.Rd man/SequenceContigsInterface.Rd man/SraDataFile.Rd man/SraDataSet.Rd man/TopHat2Alignment.Rd man/TotalCnBinnedCounting.Rd man/aroma.seq-package.Rd man/bowtie2.Rd man/bowtie2Build.Rd man/buildBowtie2IndexSet.FastaReferenceFile.Rd man/buildBwaIndexSet.FastaReferenceFile.Rd man/buildDictionary.FastaReferenceFile.Rd man/buildIndex.FastaReferenceFile.Rd man/buildTopHat2TranscriptomeIndexSet.Bowtie2IndexSet.Rd man/bwaAln.Rd man/bwaIndex.Rd man/bwaIndexPrefix.Rd man/bwaSampe.Rd man/bwaSamse.Rd man/byOrganism.FastaReferenceFile.Rd man/byOrganism.GtfDataFile.Rd man/capabilitiesOf.AromaSeq.Rd man/convertToBam.Rd man/convertToSam.Rd man/createIndexPrefix.Rd man/cuffdiff.Rd man/cufflinks.Rd man/doBWA.Rd man/doBowtie2.Rd man/doDownsample.Rd man/doHTSeqCount.Rd man/doQDNAseq.Rd man/doTopHat2.Rd man/fastQC.Rd man/fastqDump.Rd man/findCmd.Rd man/findCmdv.Rd man/findExternal.Rd man/findFilesTodo.Rd man/gatk.Rd man/getOutputDataSet.Rd man/htseqCount.Rd man/normalizeGcContent.Rd man/onExit.Rd man/process.Bowtie2Alignment.Rd man/process.BwaAlignment.Rd man/readDGE.HTSeqCountDataSet.Rd man/readSeqFile.Rd man/samtoolsFaidx.Rd man/samtoolsMpileup.Rd man/samtoolsSort.Rd man/samtoolsView.Rd man/setupExampleData.Rd man/sortByName.Rd man/sortByPosition.Rd man/systemBWA.Rd man/systemBowtie2.Rd man/systemBowtie2Build.Rd man/systemCuffdiff.Rd man/systemCufflinks.Rd man/systemFastQC.Rd man/systemFastqDump.Rd man/systemGATK.Rd man/systemGenericCmd.Rd man/systemHTSeqCount.Rd man/systemJava.Rd man/systemJavaJar.Rd man/systemPicard.Rd man/systemSamtools.Rd man/systemSraToolkit.Rd man/systemTopHat.Rd man/systemTopHatBuild.Rd man/tophat.Rd man/validate.BamDataFile.Rd man/writeFastaReferenceFile.FastaReferenceSet.Rd tests/BamDataSet.R tests/BamDownsampler.R tests/BamMerger,future.R tests/BamMerger.R tests/BinnedGcNormalization,SE,future.R tests/Bowtie2Alignment,PE,groupBy.R tests/Bowtie2Alignment,PE.R tests/Bowtie2Alignment,SE.R tests/BwaAlignment,PE,split.R tests/BwaAlignment,PE.R tests/BwaAlignment,SE.R tests/BwaIndexSet.R tests/FastaReferenceFile.R tests/FastqDataFile,split.R tests/FastqDataSet,PE.R tests/FastqDataSet,SE.R tests/FastqDataSet,directoryStructure.R tests/FastqDataSet,reports,FastQC.R tests/FastqDataSet,reports,qrqc,future.R tests/FastqDownsampler,future.R tests/FastqDownsampler.R tests/GtfDataFile.R tests/TopHat2Alignment,PE,HTSeqCounting,groupBy.R tests/TopHat2Alignment,PE,future.R tests/TopHat2Alignment,PE.R tests/TotalCnBinnedCounting,PE.R tests/agsub.R tests/bowtie2.R tests/bwa.R tests/capabilities.R tests/countNucleotides.R tests/doBWA,future.R tests/doBWA,realign.R tests/doBWA.R tests/doBowtie2,future.R tests/doBowtie2.R tests/doQDNASeq,future.R tests/doQDNASeq.R tests/doTopHat2,PE.R tests/doTopHat2,doHTSeqCount,PE.R tests/gatk,2.R tests/gatk.R tests/getFastaReferenceFile.R tests/readSeqFile.R tests/tophat2.R