Files in uzh/ezRun
An R meta-package for the analysis of Next Generation Sequencing Data
.gitignore
CodingStyle.md
DESCRIPTION
LICENSE
NAMESPACE
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-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-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-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-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/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-genome.R
R/util.R
R/vcf.R
R/zzz.R
README.md
inst/docs/SecondRef.md
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.gtf
inst/extdata/genes_annotation_byGene.txt
inst/extdata/genes_annotation_byTranscript.txt
inst/extdata/genome-chromsizes.txt
inst/extdata/genome.dict
inst/extdata/genome.fa
inst/extdata/genome.fa.fai
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_countqc/dataset.tsv
inst/extdata/yeast_10k_STAR_countqc/input_dataset.tsv
inst/extdata/yeast_10k_STAR_countqc/parameters.tsv
inst/extdata/yeast_10k_STAR_countqc/scripts/QC_FeatureCounts_42287.sh
inst/extdata/yeast_10k_STAR_countqc/scripts/QC_FeatureCounts_42287.sh_20191217150045849_e.log
inst/extdata/yeast_10k_STAR_countqc/scripts/QC_FeatureCounts_42287.sh_20191217150045849_o.log
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_deseq2/dataset.tsv
inst/extdata/yeast_10k_STAR_deseq2/input_dataset.tsv
inst/extdata/yeast_10k_STAR_deseq2/parameters.tsv
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/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/banner.png
inst/templates/banner.txt
inst/templates/coordinates_data.tsv
inst/templates/excerpt.Rmd
inst/templates/fgcz.css
inst/templates/fgcz_header.html
inst/templates/gatkRnaHaplotyper.Rmd
inst/templates/igvTemplate.html
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/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-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-testEzRun.sh
script/dev-utils.R
script/dev_nightlyTest.sh
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_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/ReferenceGenomeFolders.Rmd
vignettes/RnaSeqWithAdditionalSpecies.Rmd
