Files in uzh/ezRun
An R meta-package for the analysis of Next Generation Sequencing Data

DESCRIPTION
LICENSE
NAMESPACE
R/00defaults.R R/01classes.R R/02references.R R/03results.R R/Picard.R R/annotation.r R/app-AtacENCODE.R R/app-AtacSeqQC.R R/app-BamPreview.R R/app-CNVnator.R R/app-DEXSeqAnalysis.R R/app-DnaQC.R R/app-GenericPhyloseqAnalysis.R R/app-HOMER.R R/app-JunctionSeq.R R/app-Metaquast.R R/app-MothurDataAnalysisReport.R R/app-MothurDataClean.R R/app-MothurDataCleanBatch.R R/app-MothurDataCleanIllumina.R R/app-MothurErrorEstimateAndCluster.R R/app-MothurStep1Sample.R R/app-MothurStep1SampleReport.R R/app-MothurStep2Dataset.R R/app-MothurStep2DatasetReport.R R/app-PhyloseqAnalysis.R R/app-RnaBamStats.R R/app-SCCountQC.R R/app-SCFastQC.R R/app-SCRNAVelocity.R R/app-SCReport.R R/app-Uparse.R R/app-VirDetect.R R/app-ataqv.R R/app-canu.R R/app-cellRanger.R R/app-chipStats.R R/app-countOverlaps.r R/app-countQC.R R/app-deseq2TwoGroups.R R/app-edgerTwoGroups.R R/app-fastQC.R R/app-fastqscreen.R R/app-featureCounts.R R/app-flash.R R/app-gatkDnaHaplotyper.R R/app-gatkRna.R R/app-gatkRnaHaplotyper.R R/app-hgap3.R R/app-joinGenoTypes.R R/app-kallisto.R R/app-limma.R R/app-macs2.R R/app-mapping.r R/app-megahit.R R/app-meme.R R/app-metagenomeAnnotationQC.R R/app-metaspades.R R/app-mpileup.R R/app-ncpro.R R/app-quast.R R/app-resequencing.R R/app-rsem.R R/app-salmon.R R/app-scCount.R R/app-scMapping.R R/app-scater.R R/app-spades.R R/app-splitAndCluster.R R/app-subreads.R R/app-targetEnrichmentQC.R R/app-transcript-coverage.R R/app-transcriptome-mapping.R R/app-trim.R R/app-trinity.R R/bamStats-reports.r R/bamUtils.R R/bamio.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/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/rangesTools.r R/rawData.R R/reports.R R/riboSeq.R R/stats.r R/system.R R/twoGroups.R R/util-genome.R R/util.r R/vcf.r R/zzz.R README.md inst/doc/ReferenceGenomeFolders.R inst/doc/ReferenceGenomeFolders.Rmd
inst/doc/ReferenceGenomeFolders.html
inst/doc/UserManual.R inst/doc/UserManual.Rmd
inst/doc/UserManual.html
inst/extdata/EZ_GLOBAL_VARIABLES.txt
inst/extdata/EZ_PARAM_DEFAULTS.txt
inst/extdata/GATK/RnaFilters.txt
inst/extdata/GATK/RnaGtFilters.txt
inst/extdata/GATK/VariantCallingRna.scala
inst/extdata/banner.png
inst/extdata/enrichr.js
inst/extdata/enrichr_libnames.txt
inst/extdata/genes.bed
inst/extdata/genes.gtf
inst/extdata/genes_annotation.txt
inst/extdata/genome.fa
inst/extdata/hgap3_settings.xml
inst/extdata/igvTemplate.jnlp
inst/extdata/phix_2k/SRR2937443_R1.fastq.gz
inst/extdata/phix_2k/SRR2937443_R2.fastq.gz
inst/extdata/phix_2k/dataset.tsv
inst/extdata/popup.js
inst/extdata/resequencing_settings.xml
inst/extdata/smRNA_250k/dataset.tsv
inst/extdata/smRNA_250k/datasetWithAdapter.tsv
inst/extdata/smRNA_250k/test1_R1.fastq.gz
inst/extdata/smRNA_250k/test2_R1.fastq.gz
inst/extdata/subreads_settings.xml
inst/extdata/ventricles_100k/MutantSample_1_R1.fastq.gz
inst/extdata/ventricles_100k/MutantSample_1_R2.fastq.gz
inst/extdata/ventricles_100k/MutantSample_3_R1.fastq.gz
inst/extdata/ventricles_100k/MutantSample_3_R2.fastq.gz
inst/extdata/ventricles_100k/WildSample_1_R1.fastq.gz
inst/extdata/ventricles_100k/WildSample_1_R2.fastq.gz
inst/extdata/ventricles_100k/WildSample_2_R1.fastq.gz
inst/extdata/ventricles_100k/WildSample_2_R2.fastq.gz
inst/extdata/ventricles_100k/dataset.tsv
inst/extdata/ventricles_10k/MutantSample_1_R1.fastq.gz
inst/extdata/ventricles_10k/MutantSample_1_R2.fastq.gz
inst/extdata/ventricles_10k/MutantSample_3_R1.fastq.gz
inst/extdata/ventricles_10k/MutantSample_3_R2.fastq.gz
inst/extdata/ventricles_10k/WildSample_1_R1.fastq.gz
inst/extdata/ventricles_10k/WildSample_1_R2.fastq.gz
inst/extdata/ventricles_10k/WildSample_2_R1.fastq.gz
inst/extdata/ventricles_10k/WildSample_2_R2.fastq.gz
inst/extdata/ventricles_10k/dataset.tsv
inst/extdata/yeast_10k/.DS_Store
inst/extdata/yeast_10k/dataset.tsv
inst/extdata/yeast_10k/mut_1_R1.fastq.gz
inst/extdata/yeast_10k/mut_1_R2.fastq.gz
inst/extdata/yeast_10k/mut_2_R1.fastq.gz
inst/extdata/yeast_10k/mut_2_R2.fastq.gz
inst/extdata/yeast_10k/wt_1_R1.fastq.gz
inst/extdata/yeast_10k/wt_1_R2.fastq.gz
inst/extdata/yeast_10k/wt_2_R1.fastq.gz
inst/extdata/yeast_10k/wt_2_R2.fastq.gz
inst/extdata/yeast_10k_Bowtie2Transcriptome/dataset.tsv
inst/extdata/yeast_10k_Bowtie2Transcriptome/input_dataset.tsv
inst/extdata/yeast_10k_Bowtie2Transcriptome/mut_1.bam
inst/extdata/yeast_10k_Bowtie2Transcriptome/mut_1.bam.bai
inst/extdata/yeast_10k_Bowtie2Transcriptome/mut_2.bam
inst/extdata/yeast_10k_Bowtie2Transcriptome/mut_2.bam.bai
inst/extdata/yeast_10k_Bowtie2Transcriptome/parameters.tsv
inst/extdata/yeast_10k_Bowtie2Transcriptome/wt_1.bam
inst/extdata/yeast_10k_Bowtie2Transcriptome/wt_1.bam.bai
inst/extdata/yeast_10k_Bowtie2Transcriptome/wt_2.bam
inst/extdata/yeast_10k_Bowtie2Transcriptome/wt_2.bam.bai
inst/extdata/yeast_10k_STAR/dataset.tsv
inst/extdata/yeast_10k_STAR/input_dataset.tsv
inst/extdata/yeast_10k_STAR/mut_1-igv.jnlp
inst/extdata/yeast_10k_STAR/mut_1-igv.xml
inst/extdata/yeast_10k_STAR/mut_1.bam
inst/extdata/yeast_10k_STAR/mut_1.bam.bai
inst/extdata/yeast_10k_STAR/mut_2-igv.jnlp
inst/extdata/yeast_10k_STAR/mut_2-igv.xml
inst/extdata/yeast_10k_STAR/mut_2.bam
inst/extdata/yeast_10k_STAR/mut_2.bam.bai
inst/extdata/yeast_10k_STAR/parameters.tsv
inst/extdata/yeast_10k_STAR/wt_1-igv.jnlp
inst/extdata/yeast_10k_STAR/wt_1-igv.xml
inst/extdata/yeast_10k_STAR/wt_1.bam
inst/extdata/yeast_10k_STAR/wt_1.bam.bai
inst/extdata/yeast_10k_STAR/wt_2-igv.jnlp
inst/extdata/yeast_10k_STAR/wt_2-igv.xml
inst/extdata/yeast_10k_STAR/wt_2.bam
inst/extdata/yeast_10k_STAR/wt_2.bam.bai
inst/extdata/yeast_10k_STAR_counts/dataset.tsv
inst/extdata/yeast_10k_STAR_counts/input_dataset.tsv
inst/extdata/yeast_10k_STAR_counts/mut_1-stats.txt
inst/extdata/yeast_10k_STAR_counts/mut_1.txt
inst/extdata/yeast_10k_STAR_counts/mut_2-stats.txt
inst/extdata/yeast_10k_STAR_counts/mut_2.txt
inst/extdata/yeast_10k_STAR_counts/parameters.tsv
inst/extdata/yeast_10k_STAR_counts/wt_1-stats.txt
inst/extdata/yeast_10k_STAR_counts/wt_1.txt
inst/extdata/yeast_10k_STAR_counts/wt_2-stats.txt
inst/extdata/yeast_10k_STAR_counts/wt_2.txt
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/00index.html
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/banner.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/dataset.tsv
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/mut--over--wt-FDR-volcano.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/mut--over--wt-pValueHist.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/mut--over--wt-scatter.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/mut--over--wt-volcano.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/mut-over-wt-scatter.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/mut-scatter.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/result--mut--over--wt.txt
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/result--mut--over--wt.zip
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/scalingfactors.txt
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/sessionInfo.txt
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/wt-over-mut-scatter.png
inst/extdata/yeast_10k_STAR_counts_deseq2/DESeq2--mut--over--wt/wt-scatter.png
inst/extdata/yeast_10k_STAR_counts_deseq2/dataset.tsv
inst/extdata/yeast_10k_STAR_counts_deseq2/input_dataset.tsv
inst/extdata/yeast_10k_STAR_counts_deseq2/parameters.tsv
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/00index.html
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/banner.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/dataset.tsv
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/mut--over--wt-FDR-volcano.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/mut--over--wt-pValueHist.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/mut--over--wt-scatter.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/mut--over--wt-volcano.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/mut-over-wt-scatter.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/mut-scatter.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/result--mut--over--wt.txt
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/result--mut--over--wt.zip
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/scalingfactors.txt
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/sessionInfo.txt
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/wt-over-mut-scatter.png
inst/extdata/yeast_10k_STAR_counts_edger/EdgeR--mut--over--wt/wt-scatter.png
inst/extdata/yeast_10k_STAR_counts_edger/dataset.tsv
inst/extdata/yeast_10k_STAR_counts_edger/input_dataset.tsv
inst/extdata/yeast_10k_STAR_counts_edger/parameters.tsv
inst/templates/AtacSeqQC.Rmd inst/templates/CountQC.R inst/templates/CountQC.Rmd inst/templates/CountQC_goClusterTable.Rmd inst/templates/DnaQC.Rmd inst/templates/ErrorReport.Rmd inst/templates/FastQC.R inst/templates/FastQC.Rmd inst/templates/FastQC_overview.Rmd inst/templates/FastqScreen.R inst/templates/FastqScreen.Rmd inst/templates/MothurDataAnalysisReport.Rmd inst/templates/MothurDataClean.Rmd inst/templates/MothurDataCleanIllumina.Rmd inst/templates/MothurErrorEstimateAndCluster.Rmd inst/templates/MothurPhyloseqAnalysis.Rmd inst/templates/MothurPhyloseqAnalysisMerged.Rmd inst/templates/MothurPhyloseqGenericAnalysis.Rmd inst/templates/MothurStep1SampleReport.Rmd inst/templates/MothurStep2DatasetReport.Rmd inst/templates/MothurStep2DatasetReportNoGroup.Rmd inst/templates/PhyloseqReport.Rmd inst/templates/PhyloseqReportNoGroup.Rmd inst/templates/RNABamStats.R inst/templates/RNABamStats.Rmd inst/templates/SCCountQC.R inst/templates/SCCountQC.Rmd inst/templates/SCRNAVelocity.R inst/templates/SCRNAVelocity.Rmd inst/templates/SCReport.R inst/templates/SCReport.Rmd inst/templates/VirDetect.R inst/templates/VirDetect.Rmd
inst/templates/banner.png
inst/templates/fgcz.css
inst/templates/fgcz_header.html
inst/templates/metagenomeAnnotation.Rmd inst/templates/twoGroups.R 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/DuplicationMetrics.Rd man/EzApp-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/EzAppCanu-class.Rd man/EzAppChipStats-class.Rd man/EzAppCountOverlaps-class.Rd man/EzAppCountQC-class.Rd man/EzAppDEXSeqAnalysis-class.Rd man/EzAppDeseq2-class.Rd man/EzAppEdger-class.Rd man/EzAppEdgerMulti-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/EzAppGatkRnaHaplotyper-class.Rd man/EzAppHGAP-class.Rd man/EzAppJoinGenoTypes-class.Rd man/EzAppKallisto-class.Rd man/EzAppMEME-class.Rd man/EzAppMacs2-class.Rd man/EzAppMpileup-class.Rd man/EzAppNcpro-class.Rd man/EzAppQuast-class.Rd man/EzAppRSEM-class.Rd man/EzAppResequencing-class.Rd man/EzAppRnaBamStats-class.Rd man/EzAppSCCounts-class.Rd man/EzAppSTAR-class.Rd man/EzAppSalmon-class.Rd man/EzAppScater-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/EzDataset-class.Rd man/EzRef-class.Rd man/EzResult-class.Rd man/addCountResultSummary.Rd man/addDEXSeqCondition.Rd man/addDataset.Rd man/addGageTables.Rd man/addJavaScriptIgvStarter.Rd man/addQcScatterPlots.Rd man/addResultFile.Rd man/addSignificantCounts.Rd man/addTestScatterPlots.Rd man/addTranscriptsToGffExons.Rd man/addTxtLinksToReport.Rd man/aggregateCountsByGene.Rd man/annotatePeaks.Rd man/averageColumns.Rd man/averageRows.Rd man/bam2bw.Rd man/bam2fastq.Rd man/calmdBam.Rd man/cleanGenomeFiles.Rd man/cleanupMultiGroupsInput.Rd man/cleanupTwoGroupsInput.Rd man/clusterHeatmap.Rd man/colorClusterLabels.Rd man/computeBamStats.Rd man/computeRangeStats.Rd man/consensusPeaks.Rd man/convertGtfToGff.Rd man/countDensPlot.Rd man/countReadsInFastq.Rd man/doGo.Rd man/dupBam.Rd man/enrichrAddList.Rd man/enrichrEnrich.Rd man/expandGRanges.Rd man/ezAllPairScatter.Rd man/ezBam2bigwig.Rd man/ezBamSeqNames.Rd man/ezBuildAttributeField.Rd man/ezChromSizesFromVcf.Rd man/ezCollapse.Rd man/ezColorLegend.Rd man/ezCombineReadDatasets.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/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/gageSigGenes.Rd man/getBWAReference.Rd man/getBamMultiMatching.Rd man/getBlacklistedRegions.Rd man/getBlueRedScale.Rd man/getBowtie2Reference.Rd man/getBowtie2TranscriptomeReference.Rd man/getBowtieReference.Rd man/getDupRateFromBam.Rd man/getEnrichrLibNames.Rd man/getEnsemblTypes.Rd man/getExonNumber.Rd man/getGOparents.Rd man/getGeneIdExprLinks.Rd man/getGeneMapping.Rd man/getGeneSets.Rd man/getGeneTable.Rd man/getIgvLocusLink.Rd man/getKallistoReference.Rd man/getKeggId.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/getSpeciesName.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/goClusterTable.Rd man/goStringsToList.Rd man/groupGff.Rd man/hasFilesafeCharacters.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/lGetPyScriptPaths.Rd man/lastVal.Rd man/loadCountDataset.Rd man/loadSCCountDataset.Rd man/logMessage.Rd man/makeCoordinate.Rd man/makeMinimalSingleEndReadDataset.Rd man/mioString.Rd man/mkCurlQryString.Rd man/modifyInput.Rd man/multiGroupCountComparison.Rd man/ncpro.Rd man/openBsdocReport.Rd man/parseEnrichrLibNames.Rd man/plateStatistics.Rd man/plotBamStat.Rd man/postProcessResults.Rd man/readNcProResult.Rd man/runCountSingleBam.Rd man/runEnrichr.Rd man/runGageAnalysis.Rd man/runNgsCountQC.Rd man/runTEQC.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/tableFromSets.Rd man/transcriptAnnoFromGtf.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/writeJavaScriptIgvStarter.Rd man/writeNgsMultiGroupReport.Rd man/writePresplicedGtf.Rd man/writeSCMM.Rd man/zipFile.Rd script/archived-scripts/03plotter.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/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/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/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.R script/archived-scripts/plotters.R
script/archived-scripts/rawData.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-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-utils.R
script/dev_nightlyTest.sh
script/enrichrLinkTest.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/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_examples.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/00readme.txt
vignettes/CustomReferenceFiles.R vignettes/CustomReferenceFiles.Rmd vignettes/ReferenceGenomeFolders.Rmd
uzh/ezRun documentation built on Dec. 12, 2018, 8:49 p.m.