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

Package index
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Functions
1125
Source code
283
Man pages
309
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uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data
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API

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

Global functions
.checkGtfForExons Source code
.countPairedBamHits Source code
.dummyFunction Source code
.ezAUC Source code
.ezMergeLeftRightAlignments Man page Source code
.ezMethodBam2Fastq_NotPerRG Source code
.ezMethodBam2Fastq_PerRG Source code
.ezROC Source code
.ezROCtest Source code
.ezSequenceFromRanges Source code
.ezSgelapply Source code
.gatkHaplotypeCaller Source code
.getAvgProfileByOrientation Source code
.getGoTermsAsTd Source code
.getProfileMatrixForRanges Source code
.getRleFromRanges Source code
.makeSeqAnnoFromCounts Source code
.makeTailEffectPlots Source code
.onLoad Source code
.runGatk Source code
.waitUntilFileExists Source code
CollectAlignmentSummaryMetrics Man page Source code
CollectRnaSeqMetrics Man page Source code
CoverageVarFunction Source code
Create_ChIP_QCPlots_ind Source code
DADA2CreateSeqTab Man page Source code
DADA2mergeSeqTabs Man page Source code
DuplicationMetrics Man page Source code
EzApp Man page
EzApp-class Man page
EzAppATACSeqQC Man page
EzAppATACSeqQC-class Man page
EzAppBWA Man page
EzAppBWA-class Man page
EzAppBamPreview Man page
EzAppBamPreview-class Man page
EzAppBismark Man page
EzAppBismark-class Man page
EzAppBowtie Man page
EzAppBowtie-class Man page
EzAppBowtie2 Man page
EzAppBowtie2-class Man page
EzAppBowtie2Transcriptome Man page
EzAppBowtie2Transcriptome-class Man page
EzAppCNVnator Man page
EzAppCNVnator-class Man page
EzAppCanu Man page
EzAppCanu-class Man page
EzAppCellRanger Man page
EzAppCellRanger-class Man page
EzAppChipStats Man page
EzAppChipStats-class Man page
EzAppCountOverlaps Man page
EzAppCountOverlaps-class Man page
EzAppCountQC Man page
EzAppCountQC-class Man page
EzAppDADA2Step1Sample Man page
EzAppDADA2Step1Sample-class Man page
EzAppDADA2Step2Dataset Man page
EzAppDADA2Step2Dataset-class Man page
EzAppDEXSeqAnalysis Man page
EzAppDEXSeqAnalysis-class Man page
EzAppDeseq2 Man page
EzAppDeseq2-class Man page
EzAppDnaQC Man page
EzAppDnaQC-class Man page
EzAppENA Man page
EzAppENA-class Man page
EzAppEdger Man page
EzAppEdger-class Man page
EzAppFastqScreen Man page
EzAppFastqScreen-class Man page
EzAppFastqc Man page
EzAppFastqc-class Man page
EzAppFeatureCounts Man page Man page
EzAppFeatureCounts-class Man page
EzAppFlash Man page
EzAppFlash-class Man page
EzAppGatkDnaHaplotyper Man page
EzAppGatkDnaHaplotyper-class Man page
EzAppGatkRna Man page
EzAppGatkRna-class Man page
EzAppHGAP Man page
EzAppHGAP-class Man page
EzAppJoinGenoTypes Man page
EzAppJoinGenoTypes-class Man page
EzAppJunctionSeq Man page
EzAppJunctionSeq-class Man page
EzAppKallisto Man page
EzAppKallisto-class Man page
EzAppKraken Man page
EzAppKraken-class Man page
EzAppMEME Man page
EzAppMEME-class Man page
EzAppMacs2 Man page
EzAppMacs2-class Man page
EzAppMegahit Man page
EzAppMegahit-class Man page
EzAppMetagenomeAnnotationQC Man page
EzAppMetagenomeAnnotationQC-class Man page
EzAppMetaquast Man page
EzAppMetaquast-class Man page
EzAppMetaspades Man page
EzAppMetaspades-class Man page
EzAppMothurStep1Sample Man page
EzAppMothurStep1Sample-class Man page
EzAppMothurStep1SampleReport Man page
EzAppMothurStep1SampleReport-class Man page
EzAppMothurStep2Dataset Man page
EzAppMothurStep2Dataset-class Man page
EzAppMothurStep2DatasetReport Man page
EzAppMothurStep2DatasetReport-class Man page
EzAppMpileup Man page
EzAppMpileup-class Man page
EzAppNcpro Man page
EzAppNcpro-class Man page
EzAppPhyloSeqAnalysis Man page
EzAppPhyloSeqAnalysis-class Man page
EzAppQuast Man page
EzAppQuast-class Man page
EzAppRSEM Man page
EzAppRSEM-class Man page
EzAppResequencing Man page
EzAppResequencing-class Man page
EzAppRnaBamStats Man page
EzAppRnaBamStats-class Man page
EzAppSCCounts Man page
EzAppSCCounts-class Man page
EzAppSGSeq Man page
EzAppSGSeq-class Man page
EzAppSTAR Man page
EzAppSTAR-class Man page
EzAppSalmon Man page
EzAppSalmon-class Man page
EzAppSpades Man page
EzAppSpades-class Man page
EzAppSplitAndCluster Man page
EzAppSplitAndCluster-class Man page
EzAppSubreads Man page
EzAppSubreads-class Man page
EzAppTeqc Man page
EzAppTeqc-class Man page
EzAppTophat Man page
EzAppTophat-class Man page
EzAppTranscriptCoverage Man page
EzAppTranscriptCoverage-class Man page
EzAppTrinity Man page
EzAppTrinity-class Man page
EzAppUparse Man page
EzAppUparse-class Man page
EzAppVirDetect Man page
EzAppVirDetect-class Man page
EzDataset Man page
EzDataset-class Man page
EzRef Man page Source code
EzRef-class Man page
EzResult Man page
EzResult-class Man page
IlluminaDatasetToMothur Source code
MakeCpGDensityPlot Source code
MakeEnrichmentPlot Source code
MyTable Source code
PlotData Source code
RidgePlot.sce Source code
SingleCorPlot Source code
SpatiallyVariableFeatures_workaround Source code
StartPosTableFunction Source code
VariableFeaturePlot_mod Source code
[,EzRef,ANY,ANY,ANY-method Man page
[<-,EzRef,ANY,ANY,ANY-method Man page
abundPlot Man page Source code
addAmbientEstimateToSeurat Source code
addCellCycleToSCE Source code
addCellCycleToSeurat Source code
addCellQcToSeurat Source code
addCountResultSummary Man page
addDataset Man page
addGeneNamesEnrich Source code
addGoParents Man page Source code
addIgvSessionLink Man page
addJavaScriptIgvStarter Man page
addPromotersToGff Man page Source code
addQcScatterPlots Man page
addReplicate Man page Source code
addResultFile Man page Source code
addResultFileSE Source code
addTxtLinksToReport Man page
add_centered_title Man page Source code
aggregateCountsByGene Source code
aggregateFeatAnno Man page Source code
aggregateGoAnnotation Man page Source code
alignmentCountBarPlot Source code
all2all Source code
annotateCNVs Source code
annotatePeaks Man page Source code
atacBamProcess Source code
autoEstContTfidfMin Source code
averageColumns Man page Source code
averageRows Man page Source code
bam2bw Man page Source code
bam2fastq Man page Source code
binMyBam Source code
brewPalette Source code
buildIgvGenome Source code
buildIgvGenome,EzRef-method Man page
buildMultiConfigFile Source code
buildRefDir Source code
buildRefDir,EzRef-method Man page
calmdBam Man page Source code
cellClustNoCorrection Source code
cellsLabelsWithAUC Source code
cellsLabelsWithSingleR Source code
cellsProportion Source code
checkAndCleanAntibody Source code
chimeraSummaryPlot Man page Source code Source code
chimeraSummaryTable Man page Source code
cleanForFreeDiskSpace Source code
cleanGenomeFiles Man page Source code
cleanupTwoGroupsInput Man page Source code
closeBsdocReport Man page
clusterData Source code
clusterHeatmap Man page Source code
clusterPheatmap Source code
clusterResults Man page Source code
collectBowtie2Output Source code
collectChildren Source code
colorClusterLabels Man page Source code
colorNode Man page Source code
communityPercSummTable Man page Source code
compileEnrichmentInput Source code
computeBamStats Man page
computeBamStatsSC Source code Source code
computeDnaBamStats Man page Source code
computePathwayActivityAnalysis Source code
computeRangeStats Man page Source code
computeTFActivityAnalysis Source code
consensusPeaks Man page Source code
conservedMarkers Source code
convStepTable Man page Source code Source code
convertDiamondAnnotationToAbund Source code
convertGtfToGff Man page
countAndAssignSeqsFromFasta Man page Source code
countBamHitsSingleChrom Source code
countDensGGPlot Source code
countDensPlot Man page Source code
countIsoformsPerGene Man page Source code
countNonredundant Source code
countPairedBamHitsSingleChrom Source code
countQcScatterPlots Source code
countReadsInFastq Man page Source code
countTranscriptBam Source code
createAbundTable Source code
createCellMarker2_GeneSets Source code
createDataset Source code
createDendogramReport Source code
createGeneSets Source code
createJson Source code
createLibraryFile Source code Source code
createPangolinScript Source code
createSaturationTableForKableExtra Man page Source code
createStepConvTableForKableExtra Man page Source code
createSummaryTable Man page Source code Source code
createSummaryTableForKableExtra Man page Source code
createTSSPlot Source code
cumHistPlot Source code
datasetToMothur Man page Source code
delete_e Source code
diffExpressedGenes Source code
doEnrichr Source code
doGo Man page Source code
dupBam Man page Source code
enrichrAddList Man page Source code
enrichrEnrich Man page Source code
errorRateSummaryPlot Man page Source code Source code
expandGRanges Man page Source code
extractTopN Man page Source code
ezAllPairScatter Man page Source code
ezArrayImage Source code
ezBam2bigwig Man page Source code
ezBamSeqLengths Man page Source code
ezBamSeqNames Man page Source code
ezBuildAttributeField Man page Source code
ezCbind Source code
ezCdfPlot Source code
ezChromSizesFromVcf Man page Source code
ezColGroupMeans Source code
ezColGroupSums Source code
ezCollapse Man page Source code
ezColorLegend Man page Source code
ezColorLegendGG2 Man page Source code
ezColorMapFromDesign Source code
ezColorsFromDesign Source code
ezCombineReadDatasets Man page Source code
ezComputeBias Man page Source code
ezConditionsFromDataset Man page Source code
ezConditionsFromDesign Man page Source code
ezCorrectBias Source code
ezCorrelationPlot Man page Source code
ezCut Man page Source code
ezDesignFromDataset Man page Source code
ezDuplicated Man page Source code
ezEnricher Source code
ezFeatureAnnotation Man page Source code
ezFilterVcf Man page Source code
ezFlexTable Man page Source code
ezFrame Man page Source code
ezGSEA Source code
ezGcEffect Source code
ezGeomean Man page Source code
ezGetGoByLevels Man page Source code
ezGffAttributeField Man page
ezGoseq Man page Source code
ezGrepl Man page Source code
ezGrid Man page Source code
ezGroupGO Man page Source code
ezHead Man page Source code
ezHeatmap Man page Source code
ezIgvTemplateFile Man page Source code
ezImageFileLink Man page Source code
ezIntString Man page Source code
ezInteractiveTable Man page Source code
ezInteractiveTableRmd Man page Source code
ezIntersect Source code
ezIsAbsolutePath Man page Source code
ezIsSpecified Man page Source code
ezJobStart Man page Source code
ezLegend Man page Source code
ezLibComplexity Source code
ezLink Source code
ezLoadFeatures Man page Source code
ezLogmeanNorm Man page Source code
ezLogmeanScalingFactor Man page Source code
ezMail Man page Source code
ezMatrix Man page Source code
ezMclapply Man page Source code
ezMdsGG2 Source code
ezMdsPlot Man page Source code
ezMdsPlotly Source code
ezMedianNorm Man page Source code
ezMedianScalingFactor Man page Source code
ezMethodAtacENCODE Source code
ezMethodBWA Source code
ezMethodBWATrimmomatic Source code
ezMethodBam2Fastq Source code
ezMethodBamPreview Source code
ezMethodBdRhapsodySA Source code
ezMethodBismark Source code
ezMethodBowtie Source code
ezMethodBowtie2 Source code
ezMethodBowtie2Transcriptome Source code
ezMethodBusco Source code
ezMethodCNVnator Source code
ezMethodCanu Source code
ezMethodCellRanger Source code
ezMethodCellRangerARC Source code
ezMethodCellRangerATAC Source code
ezMethodCellRangerATACAggr Source code
ezMethodCellRangerAggr Source code
ezMethodCellRangerMulti Source code
ezMethodChipStats Source code
ezMethodCountOverlaps Source code
ezMethodCountQC Source code
ezMethodCountSpacer Source code
ezMethodCov19QC Source code
ezMethodCrisprScreenQC Source code
ezMethodDADA2Step1Sample Source code
ezMethodDEXSeqAnalysis Man page
ezMethodDeseq2 Source code
ezMethodDnaQC Source code
ezMethodEdger Source code
ezMethodExceRpt Source code
ezMethodExceRptReport Source code
ezMethodFastQC Source code
ezMethodFastQC_10x Source code
ezMethodFastpTrim Source code
ezMethodFastqScreen Source code
ezMethodFastqScreen_10x Source code
ezMethodFeatureCounts Man page Source code
ezMethodFlash Source code
ezMethodGatkDnaHaplotyper Source code
ezMethodGatkRnaHaplotyper Source code
ezMethodGce Source code
ezMethodGetEnaData Source code
ezMethodHomerDiffPeaks Source code
ezMethodInlineBarcodeDmx Source code
ezMethodJoinGenoTypes Source code
ezMethodKallisto Source code
ezMethodKraken Source code
ezMethodLimma Source code
ezMethodMEME Source code
ezMethodMacs2 Source code
ezMethodMageckCount Source code
ezMethodMageckCountQC Source code
ezMethodMageckTest Source code
ezMethodMegahit Source code
ezMethodMergeRunData Source code
ezMethodMetaQuast Source code
ezMethodMetagenomeAtlas Source code
ezMethodMetaspades Source code
ezMethodMetatranscriptomeAnalysis Source code
ezMethodMothur Source code
ezMethodMothurStep1Sample Source code
ezMethodMothurStep1SampleReport Source code
ezMethodMpileup Source code
ezMethodNanoPlot Source code
ezMethodNcpro Source code
ezMethodNestLink Source code
ezMethodONTwfArtic Source code
ezMethodONTwfSc Source code
ezMethodPbmm2 Source code
ezMethodPbsv Source code
ezMethodPhyloSeqAnalysis Source code
ezMethodPostSamsa2Analysis Source code
ezMethodPreqc Source code
ezMethodProdigal Source code
ezMethodProkka Source code
ezMethodPsortb Source code
ezMethodQIIME2 Source code
ezMethodQuast Source code
ezMethodRSEM Source code
ezMethodRnaBamStats Source code
ezMethodRnaComputeBias Source code
ezMethodRunJunctionSeqPipeline Source code
ezMethodSCCountQC Source code
ezMethodSCCounts Source code
ezMethodSCFastQC Source code
ezMethodSCFeatBarcoding Source code
ezMethodSCLabelClusters Source code
ezMethodSCTrajectoryInference Source code
ezMethodSGSeq Source code
ezMethodSTAR Source code
ezMethodSTARsolo Source code
ezMethodSamsa2 Source code
ezMethodScSCE Source code
ezMethodScSCECombine Source code
ezMethodScSCECompare Source code
ezMethodScSeurat Source code
ezMethodScSeuratCombine Source code
ezMethodScSeuratCombinedLabelClusters Source code
ezMethodScSeuratCompare Source code
ezMethodScSeuratFilterClusters Source code
ezMethodScSeuratLabelClusters Source code
ezMethodSingleCellFeatureCounts Source code
ezMethodSingleCellSTAR Source code
ezMethodSpaceRanger Source code
ezMethodSpaceRangerAggr Source code
ezMethodSpades Source code
ezMethodSpatialSeurat Source code
ezMethodSpatialSeuratCompare Source code
ezMethodSpatialSeuratSlides Source code
ezMethodSplitAndCluster Source code
ezMethodSubreads Source code
ezMethodSubsampleFastq Source code
ezMethodSubsampleReads Man page
ezMethodTeqc Source code
ezMethodTrim Man page
ezMethodTrinity Source code
ezMethodUnicycler Source code
ezMethodVPipe Source code
ezMethodVcfStats Source code
ezMethodVeloCyto Source code
ezMethodVirDetect Source code
ezMultiplicated Man page Source code
ezNorm Man page Source code
ezParam Man page Source code
ezPosSpecErrorRate Man page Source code
ezPresentFlags Man page Source code
ezProfilePlot Source code
ezQuantileNorm Man page Source code
ezRandomString Source code
ezRbind Source code
ezRead.table Man page Source code
ezReadGappedAlignments Man page Source code
ezReadGff Man page Source code
ezReadPairedAlignments Man page Source code
ezReplicateNumber Man page Source code
ezRun Man page
ezRun-package Man page
ezScaleColumns Man page Source code
ezScanBam Man page Source code
ezScatter Man page Source code
ezSessionInfo Man page Source code Source code
ezShowCol Source code
ezSmoothScatter Man page Source code
ezSortIndexBam Man page Source code
ezSplit Man page Source code
ezSplitLongLabels Man page Source code
ezSplitLongText Man page Source code
ezSystem Man page Source code
ezTagListFromNames Source code
ezThreads Man page Source code
ezTime Man page Source code
ezTranscriptDbFromRef Man page Source code
ezUnion Source code
ezUpdateMissingParam Source code
ezUtrSequences Man page Source code
ezValidFilename Man page Source code
ezValidMail Man page Source code
ezVolcano Man page Source code
ezVsnNorm Man page Source code
ezWrite Man page Source code
ezWrite.table Man page Source code
ezWriteElapsed Man page Source code
ezWriteGff Man page Source code
ezWriteVcf Man page Source code
ezXYScatter Man page Source code
ezXYScatter.2 Man page Source code
fastq2bam Source code
fastqs2bam Man page Source code
fillNaWithClosestNeighbor Source code
filterCellsAndGenes Source code
filterCellsAndGenes.Seurat Source code
filterCellsAndGenes.SingleCellExperiment Source code
filterCountsForDiffExpr Source code
filterEnrichrResults Man page Source code
filterFastqByBam Man page Source code
filteroutBam Man page Source code
findUnusedDirs Source code
fixFeatureCountsRGMatrix Source code
fixStrand Man page Source code
flipStrand Man page Source code
fragLengthReadMidDensityPlot Source code
fragmentSize Source code
galp2gal Source code
geneMeansCluster Source code
generateFlattenedFileForSGeq Man page Source code
getAdapterStats Source code
getAvgTisReadStartProfiles Source code
getBSgenomes Source code
getBWAReference Man page Source code
getBamLocally Source code
getBamMultiMatching Man page Source code
getBdWtaReference Source code
getBinColors Source code
getBismarkReference Source code
getBlacklistedRegions Man page Source code
getBlueRedScale Man page Source code
getBowtie2Reference Man page Source code
getBowtie2TranscriptomeReference Man page Source code
getBowtieReference Man page Source code
getCdsProfiles Source code
getCellCycle Source code
getCellRangerARCReference Source code
getCellRangerATACReference Source code
getCellRangerGEXReference Man page Source code
getCellRangerMultiData Source code
getCellRangerReference Source code
getCellRangerVDJReference Man page Source code
getChildTerms Source code
getCondsColors Source code
getControlSeqs Man page Source code
getCpm Man page Source code
getDupRateFromBam Man page Source code
getElapsed Man page Source code
getEnrichrLibNames Man page Source code
getEnsemblTypes Man page Source code
getExonNumber Man page Source code
getExonProfiles Source code
getFastqDirs Source code Source code Source code Source code
getFastqScreenStats Source code
getFeatureCounts Source code
getGOparents Man page Source code
getGeneIdExprLinks Man page
getGeneMapping Man page Source code
getGeneTable Man page
getGigabyteFree Man page Source code
getGigabyteTotal Source code
getGlobalDefaults Source code
getIgvGenome Man page Source code
getIgvLocusLink Man page Source code
getJobConfig Source code
getJunctionPlotsFromBam Man page Source code
getKallistoReference Man page Source code
getMageckReference Source code
getOrganism Source code
getOrganism,EzRef-method Man page
getPbmm2Reference Source code
getPerplexity Source code
getPosErrorFromBam Man page Source code
getQualityMatrix Man page Source code
getRSEMReference Man page Source code
getRangeValues Man page Source code
getRangesCoverage Man page Source code
getRefBuildMap Source code
getReferenceFeaturesBed Man page Source code
getRpkm Man page Source code
getSTARReference Man page Source code
getSTARSoloReference Source code
getSalmonReference Man page
getSampleColors Man page Source code
getSampleLty Man page Source code
getSampleMultiplexFiles Source code
getSamplePch Man page Source code
getSeuratMarkers Source code
getSeuratMarkersAndAnnotate Source code
getSeuratVarsToRegress Source code
getSignal Man page Source code
getSignificantCountsTable Source code
getSignificantCountsTableSE Source code
getSignificantFoldChangeCountsTable Source code
getSignificantFoldChangeCountsTableSE Source code
getSpatialSeuratMarkersAndAnnotate Source code
getSpecies Source code
getStatsFromBam Man page Source code
getStatsFromBamParallel Man page Source code
getStatsFromBamSingleChrom Man page Source code
getSuffix Man page Source code
getTargetRanges Source code
getTargetTypeCounts Man page Source code
getTpm Man page Source code
getTranscript2Gene Man page Source code
getTranscriptCoverage Man page Source code
getTranscriptGcAndWidth Man page Source code
getTranscriptProfiles Source code
getTranscriptSequences Man page Source code
getTranslationInitiationSite Source code
getTuxedoLibraryType Man page Source code
getTypeCountTable Source code
getTypeCoverageTable Source code
get_rRNA_Strandness Source code
gffGroupToRanges Man page Source code
gffToRanges Man page Source code
gffTrimSingleTranscript Man page Source code
gffTrimTranscripts Man page Source code
gg_color_hue Source code
goClusterResults Man page Source code
goClusterTableRmd Man page Source code
goGroupBarPlot Source code
goStringsToList Man page Source code
goUpDownTables Source code
groupGff Man page Source code
groupModRichPlot Man page Source code
gtfByTxTypes Source code
hasFilesafeCharacters Man page Source code
hasGeneMapping Man page Source code
hasGoAnnotation Man page Source code
heatmapForPhylotseqPlotPheatmap Man page Source code
heatmapPlate Man page Source code
imgLinks Man page
import.Macs2Peaks Man page Source code
initialize,EzRef-method Man page
intHist Man page Source code
interleaveMatricesByColumn Man page Source code
interproscanFileReport Source code
inverseMapping Man page Source code
isError Man page Source code
isValidCigar Man page Source code
isValidEnvironments Source code
keepOnlyCoreFiles Source code
lGetGlobalCountParam Man page Source code
lastVal Man page Source code
listBiotypes Source code
listOfAbundMerge Source code
load10xData Source code
load10xSC_seurat Source code
load10xSpatialData Source code
loadCountDataset Man page Source code
loadMageckCountDataset Source code
loadSCCountDataset Man page Source code
logMessage Man page Source code
makeBdRhapRefYmlFile Source code
makeBdYmlFile Source code
makeBiomartFile Source code
makeCoordinate Man page Source code
makeCountResultSummary Source code
makeExtraControlSeqGR Man page Source code
makeFeatAnnoEnsembl Source code
makeMinimalPairedEndReadDataset Man page Source code
makeMinimalSingleEndReadDataset Man page Source code
makeMultiMapping Man page Source code
makeResultFile Source code
makeRmdReport Source code
makeSGSeqtxdbObject Man page Source code
makeSTARsoloCmd Source code
makeScatterplot Source code
makeSignificantCounts Source code
makeSummarizedExperiment Source code
makeTagDirectory Source code
makeTestScatterData Source code
makeWebgestaltFiles Source code
mapGoToSlim Source code
mapToCovidGenome Source code
map_and_count_refseq Source code
map_and_count_virus Source code
mergeBamAlignments Source code
mergeSummaryBinFiles Source code
metagMetatrDifferentialAnalysis_tableAndPlots Source code
mioString Man page Source code
mixedDatasetToMothur Man page Source code
mkCurlQryString Man page Source code
modifyInput Man page Source code
myFisherTest Source code
ncpro Man page Source code
newWindowLink Man page
normalized.distr Source code
openBsdocReport Man page
ordPlot Man page Source code
orgFuncHeatmapPrep Source code
orgFuncHeatmaptoBoxPlotPrep Source code
otuSaturationTable Man page Source code Source code
parseEnrichrLibNames Man page Source code
parseListOptions Source code
parseOptions Man page Source code
pasteExcerptCmd Source code
pcaForPhyloseqPlot Man page Source code
phyloSeqCommunityComp Man page Source code
phyloSeqDivPlotAndPercUnclassified Man page Source code
phyloSeqOTU Man page Source code
phyloSeqOTUFromFile Man page Source code
phyloSeqPreprocess Man page Source code
phyloSeqSample Man page Source code Source code
phyloSeqTaxa Man page Source code
phyloSeqTaxaFromFile Man page Source code
phyloSeqToDeseq2_tableAndPlots Man page Source code
plateStatistics Man page Source code
plotBarMod Man page Source code
plotCellRangerCoverage Source code
plotExogenousTaxonomyTrees Source code
plotLocusAverageCoverageProfile Source code
plotLocusCoverageProfile Man page Source code
plotPosSpecificErrorRate Source code
plotQualityHeatmapGG2 Source code
plotQualityMatrixAsHeatmapGG2 Source code
plotReadCountToLibConc Source code
plotTree Source code
posClusterMarkers Source code
posClusterMarkersSpatial Source code
posSpecErrorBam Source code
posSpecErrorMDBam Source code
postProcessResults Man page Source code
postProcessTagResults Source code
prepareFastqData Source code
prepareFilesLocallyForMothur Source code
prepareJavaTools Source code
printMessage Source code
processSamples Source code
prodigalFileReport Man page Source code
querySignificantClusterAnnotationEnrichR Source code
rarefactionPlot Man page Source code
readBam Source code
readData Source code
readNcProResult Man page
readSCMM Man page Source code
removeReadsFromFastq Man page Source code
removeSuffix Man page Source code
remove_outliers Source code
revigoUpDownTables Source code
runBasicProcessing Source code
runCountSingleBam Man page
runDeseq2 Man page Source code
runEdger Man page Source code
runEnrichr Man page Source code
runGatkPipeline Source code
runGfold Man page
runGlm Man page Source code
runJunctionSeq Source code
runKraken Source code
runLimma Source code
runQoRTs Source code
runTEQC Man page Source code
runWebgestaltGSEA Source code
saveExternalFiles Source code
scranClustering Source code
scranDiffGenes Source code
scranIntegration Source code
scranPosMarkers Source code
scranPreprocessing Source code
selectFeatures Man page Source code
separateGoIdsByOnto Man page Source code
setEnvironments Source code
setwdNew Man page Source code
seuratClustering Source code
seuratClusteringHTO Source code
seuratClusteringV3 Source code
seuratIntegrateDataAndAnnotate Source code
seuratStandardSCTPreprocessing Source code
seuratStandardWorkflow Source code
shiftZeros Man page Source code
shrinkToRange Man page Source code
spatialMarkers Source code
splitBamByRG Man page Source code
splitByAdapters Source code
splitCoordinate Man page Source code
splitCounts Man page Source code
splitRegion Man page Source code
strandName Man page Source code
strandValue Man page Source code
subSampleRle Man page Source code
subsample Source code Source code
subsampleCountMatrix Source code
subsampleFastqFile Source code
subsetRankTopN Man page Source code
subsetTaxMod Man page
summaryConfPlot Source code
summaryFamilyPlot Source code
summaryGOPlot Source code
summaryGcContPlot Source code
summaryHeatmap Source code
summaryMatchScorePlot Man page Source code
summaryMetagenomeBins Source code
summaryRBSMotifPlot Source code
summaryRBSSpacePlot Source code
summaryScorePlot Man page Source code
tableFromSets Man page Source code
tarExtract Source code
trimGRanges Man page Source code
trimTxGtf Source code
trimWhiteSpace Man page Source code
twoGroupCountComparison Man page Source code
twoGroupsGO Man page Source code
twoGroupsGOSE Source code
txEndBias Source code
txFeatureCounts Source code
vennFromSets Man page Source code
waitForFreeDiskSpace Man page Source code
writeAnnotationFromGtf Man page
writeCountFilesToMeta Man page
writeDEXSeqReport Man page
writeErrorReport Man page Source code
writeGenericFeature Source code
writeIgvHtml Source code
writeIgvJnlp Man page Source code
writeIgvSession Man page Source code
writeIgvSessionLink Man page Source code
writeOTUgzFileForVamps Man page
writePresplicedGtf Man page
writeSCMM Man page Source code
writeVelocyto Source code
writeVelocytoFeature Source code
zipFile Man page Source code
zipWorkingDir Man page Source code
uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.

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