Files in uzh/ezRun

An R meta-package for the analysis of Next Generation Sequencing Data

CodingStyle.md R/00defaults.R R/01classes.R R/02references.R R/03results.R R/DADA2associatedFunctions.R R/Picard.R R/SGSeqAssociatedFunctions.R R/annotation.R R/app-AtacENCODE.R R/app-BDRhapsodySA.R R/app-BamPreview.R R/app-CNVnator.R R/app-Cov19QC.R R/app-CrisprScreenQCApp.R R/app-DADA2Step1Sample.R R/app-Dmrseq.R R/app-DnaQC.R R/app-ENA.R R/app-Gce.R R/app-HOMER.R R/app-JunctionSeq.R R/app-MageckCountApp.R R/app-MageckTestApp.R R/app-MetagenomeAtlas.R R/app-Mothur.R R/app-MothurStep1Sample.R R/app-MothurStep1SampleReport.R R/app-Mutect2.R R/app-NanoPlot.R R/app-NestLink.R R/app-ONTwfArtic.R R/app-ONTwfSc.R R/app-PhyloseqAnalysis.R R/app-PostSamsa2Analysis.R R/app-QIIME2.R R/app-RnaBamStats.R R/app-RnaComputeBias.R R/app-SCCountQC.R R/app-SCCounts.R R/app-SCFastQC.R R/app-SCFeatBarcoding.R R/app-SCLabelClusters.R R/app-SCTrajectoryInference.R R/app-SGseq.R R/app-STARsolo.R R/app-ScSCE.R R/app-ScSCECombine.R R/app-ScSCECompare.R R/app-ScSeurat.R R/app-ScSeuratCombine.R R/app-ScSeuratCombinedLabelClusters.R R/app-ScSeuratCompare.R R/app-ScSeuratFilterClusters.R R/app-ScSeuratLabelClusters.R R/app-SpatialSeurat.R R/app-SpatialSeuratCompare.R R/app-SpatialSeuratSlides.R R/app-VPipe.R R/app-VcfStats.R R/app-VeloCyto.R R/app-VirDetect.R R/app-busco.R R/app-canu.R R/app-cellBender.R R/app-cellRanger.R R/app-cellRangerARC.R R/app-cellRangerATAC.R R/app-cellRangerATACAggr.R R/app-cellRangerAggr.R R/app-cellRangerMulti.R R/app-chipStats.R R/app-countOverlaps.R R/app-countQC.R R/app-countSpacer.R R/app-deseq2TwoGroups.R R/app-edgerTwoGroups.R R/app-exceRpt.R R/app-exceRpt_report.R R/app-exploreMageckCounts.R R/app-fastQC.R R/app-fastQC_10x.R R/app-fastqscreen.R R/app-fastqscreen_10x.R R/app-featureCounts.R R/app-flash.R R/app-gatkDnaHaplotyper.R R/app-gatkRnaHaplotyper.R R/app-inlineBarcodeDmx.R R/app-joinGenoTypes.R R/app-kallisto.R R/app-kraken.R R/app-limmaTwoGroups.R R/app-macs2.R R/app-mapping.R R/app-megahit.R R/app-meme.R R/app-mergeRunData.R R/app-metaquast.R R/app-metaspades.R R/app-metatranscriptomeAnalysis.R R/app-mpileup.R R/app-ncpro.R R/app-pbmm2.R R/app-pbsv.R R/app-preqc.R R/app-prodigal.R R/app-prokka.R R/app-psortb.R R/app-quast.R R/app-rsem.R R/app-samsa2.R R/app-scMapping.R R/app-signalp.R R/app-spaceRanger.R R/app-spaceRangerAggr.R R/app-spades.R R/app-splitAndCluster.R R/app-subreads.R R/app-targetEnrichmentQC.R R/app-transcriptome-mapping.R R/app-trim.R R/app-trinity.R R/app-unicycler.R R/bamStats-reports.R R/bamUtils.R R/bamio.R R/cellxgene_annotation.R R/datasets.R R/enrichr.R R/fastqIO.R R/featurePlots.R R/gatk.R R/gc-effect.R R/gff.R R/go-analysis.R R/go-reports.R R/igv.R R/io.R R/libraryBiasCorrection.R R/messaging.R R/metagenomeAnnotationQC_associatedFunctions.R R/metatranscriptomicsAssociatedFunctions.R R/mothurAssociatedFunctions.R R/mothurDataCleanAssociatedFunctions.R R/mothurErrorEstimateAssociatedFunctions.R R/mothurPhyloseqAssociatedFunctions.R R/ngsPlots.R R/ngsReferenceFiles.R R/ngsTools.R R/ngsio.R R/plots-reports.R R/plots.R R/presentAnalysis.R R/qc-functions.R R/rangesTools.R R/rawData.R R/reports.R R/riboSeq.R R/sc-estimateAmbient.R R/scTools.R R/scranUtils.R R/seuratUtils.R R/stats.R R/system.R R/twoGroups.R R/util-fastq.R R/util-genome.R R/util.R R/vcf.R R/zzz.R README.md inst/docs/SecondRef.md inst/templates/CountQC.Rmd inst/templates/CountQC_goClusterTable.Rmd inst/templates/CountSpacer.Rmd inst/templates/Cov19QC.Rmd inst/templates/CrisprCountQC.Rmd inst/templates/CrisprScreenQC.Rmd inst/templates/DmrSeq.Rmd inst/templates/DnaQC.Rmd inst/templates/ErrorReport.Rmd inst/templates/FastQC.Rmd inst/templates/FastQC_overview.Rmd inst/templates/FastqScreen-2020-12-01.Rmd inst/templates/FastqScreen.Rmd inst/templates/Gce.Rmd inst/templates/MageckTest.Rmd inst/templates/MothurStep1SampleReport.Rmd inst/templates/Mpileup.Rmd inst/templates/Pbsv.Rmd inst/templates/PhyloseqReport.Rmd inst/templates/PhyloseqReportNoGroup.Rmd inst/templates/PostSamsa2.Rmd inst/templates/Qiime2Report.Rmd inst/templates/RNABamStats.Rmd inst/templates/SCCountQC.Rmd inst/templates/SCFeatBarcoding.Rmd inst/templates/SCLabelClusters.Rmd inst/templates/SCTrajectoryInference.Rmd inst/templates/ScCompareSCE.Rmd inst/templates/ScSCE.Rmd inst/templates/ScSCECombine.Rmd inst/templates/ScSeurat-SCpubr.Rmd inst/templates/ScSeurat.Rmd inst/templates/ScSeuratCombine.Rmd inst/templates/ScSeuratCompare.Rmd inst/templates/SpatialSeurat.Rmd inst/templates/SpatialSeuratSlides.Rmd inst/templates/VcfStats.Rmd inst/templates/VirDetect.Rmd inst/templates/excerpt.Rmd inst/templates/gatkRnaHaplotyper.Rmd inst/templates/metagenomeAnnotation.Rmd inst/templates/metatranscriptomicsAnalysis.Rmd inst/templates/twoGroups.Rmd inst/templates/twoGroups_goClusterTable.Rmd man-roxygen/addargs-template.R man-roxygen/app-template.R man-roxygen/bamFile-template.R man-roxygen/colors-template.R man-roxygen/connection-template.R man-roxygen/dataset-template.R man-roxygen/doc-template.R man-roxygen/getref-template.R man-roxygen/htmlFile-template.R man-roxygen/input-template.R man-roxygen/output-template.R man-roxygen/plot-template.R man-roxygen/rawData-template.R man-roxygen/result-template.R man-roxygen/roxygen-template.R man-roxygen/types-template.R man/CollectAlignmentSummaryMetrics.Rd man/CollectRnaSeqMetrics.Rd man/DADA2CreateSeqTab.Rd man/DADA2mergeSeqTabs.Rd man/DuplicationMetrics.Rd man/EzApp-class.Rd man/EzAppATACSeqQC-class.Rd man/EzAppBWA-class.Rd man/EzAppBamPreview-class.Rd man/EzAppBismark-class.Rd man/EzAppBowtie-class.Rd man/EzAppBowtie2-class.Rd man/EzAppBowtie2Transcriptome-class.Rd man/EzAppCNVnator-class.Rd man/EzAppCanu-class.Rd man/EzAppCellRanger-class.Rd man/EzAppChipStats-class.Rd man/EzAppCountOverlaps-class.Rd man/EzAppCountQC-class.Rd man/EzAppDADA2Step1Sample-class.Rd man/EzAppDADA2Step2Dataset-class.Rd man/EzAppDEXSeqAnalysis-class.Rd man/EzAppDeseq2-class.Rd man/EzAppDnaQC-class.Rd man/EzAppENA-class.Rd man/EzAppEdger-class.Rd man/EzAppFastqScreen-class.Rd man/EzAppFastqc-class.Rd man/EzAppFeatureCounts-class.Rd man/EzAppFeatureCounts.Rd man/EzAppFlash-class.Rd man/EzAppGatkDnaHaplotyper-class.Rd man/EzAppGatkRna-class.Rd man/EzAppHGAP-class.Rd man/EzAppJoinGenoTypes-class.Rd man/EzAppJunctionSeq-class.Rd man/EzAppKallisto-class.Rd man/EzAppKraken-class.Rd man/EzAppMEME-class.Rd man/EzAppMacs2-class.Rd man/EzAppMegahit-class.Rd man/EzAppMetagenomeAnnotationQC-class.Rd man/EzAppMetaquast-class.Rd man/EzAppMetaspades-class.Rd man/EzAppMothurStep1Sample-class.Rd man/EzAppMothurStep1SampleReport-class.Rd man/EzAppMothurStep2Dataset-class.Rd man/EzAppMothurStep2DatasetReport-class.Rd man/EzAppMpileup-class.Rd man/EzAppNcpro-class.Rd man/EzAppPhyloSeqAnalysis-class.Rd man/EzAppQuast-class.Rd man/EzAppRSEM-class.Rd man/EzAppResequencing-class.Rd man/EzAppRnaBamStats-class.Rd man/EzAppSCCounts-class.Rd man/EzAppSGSeq-class.Rd man/EzAppSTAR-class.Rd man/EzAppSalmon-class.Rd man/EzAppSpades-class.Rd man/EzAppSplitAndCluster-class.Rd man/EzAppSubreads-class.Rd man/EzAppTeqc-class.Rd man/EzAppTophat-class.Rd man/EzAppTranscriptCoverage-class.Rd man/EzAppTrinity-class.Rd man/EzAppUparse-class.Rd man/EzAppVirDetect-class.Rd man/EzDataset-class.Rd man/EzRef-class.Rd man/EzResult-class.Rd man/abundPlot.Rd man/addCountResultSummary.Rd man/addDataset.Rd man/addJavaScriptIgvStarter.Rd man/addQcScatterPlots.Rd man/addResultFile.Rd man/addTxtLinksToReport.Rd man/add_centered_title.Rd man/annotatePeaks.Rd man/averageColumns.Rd man/averageRows.Rd man/bam2bw.Rd man/bam2fastq.Rd man/calmdBam.Rd man/chimeraSummaryPlot.Rd man/chimeraSummaryTable.Rd man/cleanGenomeFiles.Rd man/cleanupTwoGroupsInput.Rd man/clusterHeatmap.Rd man/colorClusterLabels.Rd man/communityPercSummTable.Rd man/computeBamStats.Rd man/computeDnaBamStats.Rd man/computeRangeStats.Rd man/consensusPeaks.Rd man/convStepTable.Rd man/convertGtfToGff.Rd man/countAndAssignSeqsFromFasta.Rd man/countDensPlot.Rd man/countReadsInFastq.Rd man/createSaturationTableForKableExtra.Rd man/createStepConvTableForKableExtra.Rd man/createSummaryTable.Rd man/createSummaryTableForKableExtra.Rd man/datasetToMothur.Rd man/doGo.Rd man/dupBam.Rd man/enrichrAddList.Rd man/enrichrEnrich.Rd man/errorRateSummaryPlot.Rd man/expandGRanges.Rd man/extractTopN.Rd man/ezAllPairScatter.Rd man/ezBam2bigwig.Rd man/ezBamSeqNames.Rd man/ezBuildAttributeField.Rd man/ezChromSizesFromVcf.Rd man/ezCollapse.Rd man/ezColorLegend.Rd man/ezColorLegendGG2.Rd man/ezCombineReadDatasets.Rd man/ezComputeBias.Rd man/ezCorrelationPlot.Rd man/ezCut.Rd man/ezDesignFromDataset.Rd man/ezDuplicated.Rd man/ezFilterVcf.Rd man/ezFlexTable.Rd man/ezFrame.Rd man/ezGeomean.Rd man/ezGrepl.Rd man/ezGroupGO.Rd man/ezHead.Rd man/ezHeatmap.Rd man/ezImageFileLink.Rd man/ezIntString.Rd man/ezInteractiveTable.Rd man/ezInteractiveTableRmd.Rd man/ezIsAbsolutePath.Rd man/ezIsSpecified.Rd man/ezJobStart.Rd man/ezLegend.Rd man/ezLoadFeatures.Rd man/ezLogmeanNorm.Rd man/ezMail.Rd man/ezMatrix.Rd man/ezMclapply.Rd man/ezMdsPlot.Rd man/ezMedianNorm.Rd man/ezMethodDEXSeqAnalysis.Rd man/ezMethodSubsampleReads.Rd man/ezMethodTrim.Rd man/ezMultiplicated.Rd man/ezNorm.Rd man/ezParam.Rd man/ezPresentFlags.Rd man/ezQuantileNorm.Rd man/ezRead.table.Rd man/ezReadGappedAlignments.Rd man/ezReadGff.Rd man/ezReadPairedAlignments.Rd man/ezReplicateNumber.Rd man/ezRun-package.Rd man/ezScaleColumns.Rd man/ezScanBam.Rd man/ezScatter.Rd man/ezSessionInfo.Rd man/ezSmoothScatter.Rd man/ezSortIndexBam.Rd man/ezSplit.Rd man/ezSplitLongLabels.Rd man/ezSystem.Rd man/ezThreads.Rd man/ezTime.Rd man/ezTranscriptDbFromRef.Rd man/ezUtrSequences.Rd man/ezValidFilename.Rd man/ezValidMail.Rd man/ezVolcano.Rd man/ezVsnNorm.Rd man/ezWrite.Rd man/ezWrite.table.Rd man/ezWriteElapsed.Rd man/ezXYScatter.2.Rd man/fastqs2bam.Rd man/featAnnoIO.Rd man/filterEnrichrResults.Rd man/filterFastqByBam.Rd man/filteroutBam.Rd man/fixStrand.Rd man/generateFlattenedFileForSGeq.Rd man/getBWAReference.Rd man/getBamMultiMatching.Rd man/getBlacklistedRegions.Rd man/getBlueRedScale.Rd man/getBowtie2Reference.Rd man/getBowtie2TranscriptomeReference.Rd man/getBowtieReference.Rd man/getCellRangerGEXReference.Rd man/getDupRateFromBam.Rd man/getEnrichrLibNames.Rd man/getEnsemblTypes.Rd man/getExonNumber.Rd man/getGOparents.Rd man/getGeneIdExprLinks.Rd man/getGeneMapping.Rd man/getGeneTable.Rd man/getIgvLocusLink.Rd man/getKallistoReference.Rd man/getQualityMatrix.Rd man/getRSEMReference.Rd man/getRangeValues.Rd man/getReferenceFeaturesBed.Rd man/getRpkm.Rd man/getSTARReference.Rd man/getSalmonReference.Rd man/getSampleColors.Rd man/getSuffix.Rd man/getTranscript2Gene.Rd man/getTranscriptCoverage.Rd man/getTranscriptGcAndWidth.Rd man/getTranscriptSequences.Rd man/getTuxedoLibraryType.Rd man/gffToRanges.Rd man/gffTrimTranscripts.Rd man/gffUtilities.Rd man/goClusterTableRmd.Rd man/goStringsToList.Rd man/groupGff.Rd man/groupModRichPlot.Rd man/hasFilesafeCharacters.Rd man/heatmapForPhylotseqPlotPheatmap.Rd man/imgLinks.Rd man/import.Macs2Peaks.Rd man/intHist.Rd man/interleaveMatricesByColumn.Rd man/inverseMapping.Rd man/isError.Rd man/isValidCigar.Rd man/lGetGlobalCountParam.Rd man/lastVal.Rd man/loadCountDataset.Rd man/loadSCCountDataset.Rd man/logMessage.Rd man/makeCoordinate.Rd man/makeExtraControlSeqGR.Rd man/makeMinimalSingleEndReadDataset.Rd man/makeSGSeqtxdbObject.Rd man/mioString.Rd man/mixedDatasetToMothur.Rd man/mkCurlQryString.Rd man/modifyInput.Rd man/ncpro.Rd man/openBsdocReport.Rd man/ordPlot.Rd man/otuSaturationTable.Rd man/parseEnrichrLibNames.Rd man/pcaForPhyloseqPlot.Rd man/phyloSeqCommunityComp.Rd man/phyloSeqDivPlotAndPercUnclassified.Rd man/phyloSeqOTU.Rd man/phyloSeqOTUFromFile.Rd man/phyloSeqPreprocess.Rd man/phyloSeqSample.Rd man/phyloSeqTaxa.Rd man/phyloSeqTaxaFromFile.Rd man/phyloSeqToDeseq2_tableAndPlots.Rd man/plateStatistics.Rd man/plotBarMod.Rd man/plotLocusCoverageProfile.Rd man/postProcessResults.Rd man/prodigalFileReport.Rd man/rarefactionPlot.Rd man/readNcProResult.Rd man/runCountSingleBam.Rd man/runEnrichr.Rd man/runTEQC.Rd man/selectFeatures.Rd man/separateGoIdsByOnto.Rd man/setwdNew.Rd man/shiftZeros.Rd man/shrinkToRange.Rd man/splitBamByRG.Rd man/splitCoordinate.Rd man/splitCounts.Rd man/strandValue.Rd man/subSampleRle.Rd man/subsetRankTopN.Rd man/subsetTaxMod.Rd man/summaryMatchScorePlot.Rd man/summaryScorePlot.Rd man/tableFromSets.Rd man/trimGRanges.Rd man/trimWhiteSpace.Rd man/twoGroupCountComparison.Rd man/twoGroupsGO.Rd man/vennFromSets.Rd man/waitForFreeDiskSpace.Rd man/writeAnnotationFromGtf.Rd man/writeCountFilesToMeta.Rd man/writeDEXSeqReport.Rd man/writeErrorReport.Rd man/writeIgvJnlp.Rd man/writeIgvSession.Rd man/writeOTUgzFileForVamps.Rd man/writePresplicedGtf.Rd man/writeSCMM.Rd man/zipFile.Rd script/2019-12-03-dev-countqc.R script/archived-scripts/03plotter.R script/archived-scripts/AtacSeqQC.Rmd script/archived-scripts/CountQC_archived.Rmd script/archived-scripts/MothurStep2DatasetReport.Rmd script/archived-scripts/MothurStep2DatasetReportNoGroup.Rmd script/archived-scripts/PhyloseqReport.Rmd script/archived-scripts/PhyloseqReportNoGroup.Rmd script/archived-scripts/SCMultipleSamples.Rmd script/archived-scripts/SCMultipleSamplesAndGroups.Rmd script/archived-scripts/SCMultipleSamplesOneGroup.Rmd script/archived-scripts/SCOneSample.Rmd script/archived-scripts/SCRNAVelocity.Rmd script/archived-scripts/SCReport.Rmd script/archived-scripts/SCReportMerging.Rmd script/archived-scripts/SCScran.Rmd script/archived-scripts/SCScranIntegration.Rmd script/archived-scripts/SCSeurat.Rmd script/archived-scripts/annotation.R script/archived-scripts/app-AtacSeqQC.R script/archived-scripts/app-DADA2Step2Dataset.R script/archived-scripts/app-DEXSeqAnalysis.R script/archived-scripts/app-Metaquast.R script/archived-scripts/app-MothurStep2Dataset.R script/archived-scripts/app-MothurStep2DatasetReport.R script/archived-scripts/app-PhyloseqAnalysis.R script/archived-scripts/app-SCDifferentialState.R script/archived-scripts/app-SCMultipleSamples.R script/archived-scripts/app-SCMultipleSamplesAndGroups.R script/archived-scripts/app-SCMultipleSamplesOneGroup.R script/archived-scripts/app-SCOneSample.R script/archived-scripts/app-SCRNAVelocity.R script/archived-scripts/app-SCReport.R script/archived-scripts/app-SCReportMerging.R script/archived-scripts/app-SCScran.R script/archived-scripts/app-SCScranIntegration.R script/archived-scripts/app-Uparse.R script/archived-scripts/app-ataqv.R script/archived-scripts/app-countQC-reportRs.R script/archived-scripts/app-edgerMultiGroups.R script/archived-scripts/app-fastQC-ReporteRs.R script/archived-scripts/app-fastqscreen.R script/archived-scripts/app-gatkRna.R script/archived-scripts/app-gatkRnaHaplotyper.R script/archived-scripts/app-hgap3.R script/archived-scripts/app-mapping.R script/archived-scripts/app-metagenomeAnnotationQC.R script/archived-scripts/app-metatranscriptomeAnalysis.R script/archived-scripts/app-resequencing.R script/archived-scripts/app-salmon.R script/archived-scripts/app-scater.R script/archived-scripts/app-transcript-coverage.R script/archived-scripts/bamStats-reports.R script/archived-scripts/bamio.R script/archived-scripts/dev-dataset-refclass.R script/archived-scripts/dev-test_fastqscreen.R script/archived-scripts/gage-reports.R script/archived-scripts/gage.r script/archived-scripts/gff.R script/archived-scripts/go-reports-archive.R script/archived-scripts/heatmap3.R script/archived-scripts/htmlOutput.r script/archived-scripts/interactivePlots.R script/archived-scripts/interactiveTables.R script/archived-scripts/metatranscriptomicsAnalysis.Rmd script/archived-scripts/ngsio.R script/archived-scripts/old-chipStats.R script/archived-scripts/old-edgerMultiGroups.R script/archived-scripts/old-gage.R script/archived-scripts/old-gatkRnaHaplotyper.R script/archived-scripts/planForGGplots.R script/archived-scripts/planForPlots-20151029.R script/archived-scripts/planForPlots.R script/archived-scripts/plots-reports.R script/archived-scripts/plots.R script/archived-scripts/plotters.R script/archived-scripts/reports-archive.R script/archived-scripts/tablesWithinTables.R script/archived-scripts/twoGroups.R script/check-Picard-measures.R script/debug-CellRanger.R script/debug-CellRangerATAC.R script/debug-CellRangerAggr.R script/debug-FeatureCounts.R script/debug-RNABamStats.R script/debug-RSEM.R script/debug-STAR.R script/debug-atac.R script/debug-bwa.R script/debug-go.r script/debug-scRNA.R script/dev-fqscreen.R script/dev-utils.R script/make_ventricles_10k.R script/make_yeast_10k.R script/runningLongTests.R script/smoScaAndInteractivePlots.R script/test-mpileup-20160304.r script/test_DEXSeqAnalysis.R tests/test_gtfExtend.R tests/testthat.R tests/testthat/test_DeResults.R tests/testthat/test_annotation.R tests/testthat/test_apps-ChIP.R tests/testthat/test_apps-count+bam.R tests/testthat/test_apps-diffExpression.R tests/testthat/test_apps-mapping.R tests/testthat/test_apps-smRna.R tests/testthat/test_apps-transcriptome-mapping.R tests/testthat/test_apps-variant.R tests/testthat/test_bam+rawData.R tests/testthat/test_datasets.R tests/testthat/test_defaultsAndClasses.R tests/testthat/test_globalVariables.R tests/testthat/test_io.R tests/testthat/test_messaging.R tests/testthat/test_misc.R tests/testthat/test_plots.R tests/testthat/test_reports.R tests/testthat/test_tools.R tests/testthat/test_util.R vignettes/ReferenceGenomeFolders.Rmd vignettes/RnaSeqWithAdditionalSpecies.Rmd