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

Global functions
.ezMergeLeftRightAlignments Man page
.getGoTermsAsTd Man page
CollectAlignmentSummaryMetrics Man page Source code
CollectRnaSeqMetrics Man page Source code
CoverageVarFunction Source code
Create_ChIP_QCPlots_ind Source code
DEXSeqCounting Source code
DuplicationMetrics Man page Source code
EzApp Man page
EzApp-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
EzAppCanu Man page
EzAppCanu-class Man page
EzAppChipStats Man page
EzAppChipStats-class Man page
EzAppCountOverlaps Man page
EzAppCountOverlaps-class Man page
EzAppCountQC Man page
EzAppCountQC-class Man page
EzAppDEXSeqAnalysis Man page
EzAppDEXSeqAnalysis-class Man page
EzAppDeseq2 Man page
EzAppDeseq2-class Man page
EzAppEdger Man page
EzAppEdger-class Man page
EzAppEdgerMulti Man page
EzAppEdgerMulti-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
EzAppGatkRnaHaplotyper Man page
EzAppGatkRnaHaplotyper-class Man page
EzAppHGAP Man page
EzAppHGAP-class Man page
EzAppJoinGenoTypes Man page
EzAppJoinGenoTypes-class Man page
EzAppKallisto Man page
EzAppKallisto-class Man page
EzAppMEME Man page
EzAppMEME-class Man page
EzAppMacs2 Man page
EzAppMacs2-class Man page
EzAppMpileup Man page
EzAppMpileup-class Man page
EzAppNcpro Man page
EzAppNcpro-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
EzAppSTAR Man page
EzAppSTAR-class Man page
EzAppSalmon Man page
EzAppSalmon-class Man page
EzAppScater Man page
EzAppScater-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
EzDataset Man page
EzDataset-class Man page
EzRef Man page
EzRef-class Man page
EzResult Man page
EzResult-class Man page
IlluminaDatasetToMothur Source code
MakeCpGDensityPlot Source code
MakeEnrichmentPlot Source code
MyTable Source code
StartPosTableFunction Source code
[,EzRef,ANY,ANY,ANY-method Man page
[<-,EzRef,ANY,ANY,ANY-method Man page
aboveMinExprSamples Source code
addCountResultSummary Man page Source code
addCountResultSummarySE Source code
addDEXSeqCondition Man page
addDataset Man page Source code
addGageTables Man page
addGeneNamesEnrich Source code
addGoParents Man page Source code
addIgvSessionLink Man page Source code
addJavaScriptIgvStarter Man page Source code
addPromotersToGff Man page Source code
addQcScatterPlots Man page Source code
addReplicate Man page Source code
addResultFile Man page Source code
addResultFileSE Source code
addSignificantCounts Man page Source code
addSignificantCountsSE Source code
addTestScatterPlots Man page Source code
addTestScatterPlotsSE Source code
addTranscriptsToGffExons Man page Source code
addTxtLinksToReport Man page Source code
aggregateCountsByGene Man page Source code
aggregateFeatAnno Man page Source code
aggregateGoAnnotation Man page Source code
alignmentCountBarPlot Source code
annotateCNVs Source code
annotatePeaks Man page Source code
atacBamProcess 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
buildIgvGenome,EzRef-method Man page
buildRefDir,EzRef-method Man page
calmdBam Man page Source code
checkGtfForExons Source code
chimeraSummaryPlot Source code
cleanForFreeDiskSpace Source code
cleanGenomeFiles Man page Source code
cleanOldestDir Source code
cleanupMultiGroupsInput Man page
cleanupTwoGroupsInput Man page Source code
closeBsdocReport Man page Source code
clusterData Source code
clusterHeatmap Man page Source code
clusterPheatmap Source code
clusterResults Man page Source code
collectBowtie2Output Source code
collectChildren Source code
collectFastqscreenOutput Source code
colorClusterLabels Man page Source code
colorNode Man page Source code
computeBamStats Man page Source code
computeDnaBamStats Source code
computeRangeStats Man page Source code
consensusPeaks Man page Source code
convStepTable Source code Source code
convertGtfToGff Man page Source code
copyReadsLocally Source code
countBamHitsSingleChrom Source code
countDensGGPlot Source code
countDensPlot Man page Source code
countIsoformsPerGene Man page Source code
countNonredundant Source code
countPairedBamHits Source code
countPairedBamHitsSingleChrom Source code
countQcScatterPlots Source code
countReadsInFastq Man page Source code
countTranscriptBam Source code
createDendogramReport Source code
createSaturationTableForKableExtra Source code
createStepConvTableForKableExtra Source code
createSummaryTable Source code Source code
createSummaryTableForKableExtra Source code
createTSSPlot Source code
cumHistPlot Source code
datasetToMothur 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 Source code Source code
executeBowtie2CMD Source code
executeBowtie2CMD_Virus Source code
executeFastqscreenCMD Source code
expandGRanges Man page Source code
extractTopN Source code
ezAUC 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
ezCollapse Man page Source code
ezColorLegend Man page Source code
ezColorLegendGG2 Source code
ezColorMapFromDesign Source code
ezColorsFromDesign Source code
ezCombineReadDatasets 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 Source code
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 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
ezMergeLeftRightAlignments Source code
ezMethodATACSeqQC Source code
ezMethodAtacENCODE Source code
ezMethodAtaqv Source code
ezMethodBWA Source code
ezMethodBam2Fastq Source code
ezMethodBamPreview Source code
ezMethodBismark Source code
ezMethodBowtie Source code
ezMethodBowtie2 Source code
ezMethodBowtie2Transcriptome Source code
ezMethodCNVnator Source code
ezMethodCanu Source code
ezMethodCellRanger Source code
ezMethodChipStats Source code
ezMethodCountOverlaps Source code
ezMethodCountQC Source code
ezMethodDEXSeqAnalysis Man page Source code
ezMethodDeseq2 Source code
ezMethodDnaQC Source code
ezMethodEdger Source code
ezMethodFastQC Source code
ezMethodFastqScreen Source code
ezMethodFeatureCounts Man page Source code
ezMethodFlash Source code
ezMethodGatkDnaHaplotyper Source code
ezMethodGatkRna Source code
ezMethodGatkRnaHaplotyper Source code
ezMethodGenericPhyloSeqAnalysis Source code
ezMethodHGAP Source code
ezMethodHomerDiffPeaks Source code
ezMethodJoinGenoTypes Source code
ezMethodKallisto Source code
ezMethodMEME Source code
ezMethodMacs2 Source code
ezMethodMegahit Source code
ezMethodMetagenomeAnnotationQC Source code
ezMethodMetaquast Source code
ezMethodMetaspades Source code
ezMethodMothurDataAnalysisReport Source code
ezMethodMothurDataClean Source code
ezMethodMothurDataCleanBatch Source code
ezMethodMothurDataCleanIllumina Source code
ezMethodMothurErrorEstimateAndCluster Source code
ezMethodMothurStep1Sample Source code
ezMethodMothurStep1SampleReport Source code
ezMethodMothurStep2Dataset Source code
ezMethodMothurStep2DatasetReport Source code
ezMethodMpileup Source code
ezMethodNcpro Source code
ezMethodPhyloSeqAnalysis Source code
ezMethodQuast Source code
ezMethodRSEM Source code
ezMethodResequencing Source code
ezMethodRnaBamStats Source code
ezMethodRunJunctionSeqPipeline Source code
ezMethodSCCountQC Source code
ezMethodSCCounts Source code
ezMethodSCFastQC Source code
ezMethodSCRNAVelocity Source code
ezMethodSCReport Source code
ezMethodSTAR Source code
ezMethodSalmon Source code
ezMethodScater Source code
ezMethodScaterMtx Source code
ezMethodSingleCellFeatureCounts Source code
ezMethodSingleCellSTAR Source code
ezMethodSpades Source code
ezMethodSplitAndCluster Source code
ezMethodSubreads Source code
ezMethodSubsampleReads Man page Source code
ezMethodTeqc Source code
ezMethodTophat Source code
ezMethodTranscriptCoverage Source code
ezMethodTrim Man page Source code
ezMethodTrinity Source code
ezMethodUparse 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
ezROC Source code
ezROCtest 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
ezSequenceFromRanges Source code
ezSessionInfo Man page Source code
ezSgelapply 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
ezSubsampleFastq Man page
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
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
filterEnrichrResults Man page Source code
filterFastqByBam Man page Source code
filteroutBam Man page Source code
fixFeatureCountsRGMatrix Source code
fixStrand Man page Source code
flipStrand Man page Source code
fragLengthReadMidDensityPlot Source code
fragmentSize Source code
gageAnalysis Man page
gageHeatmap Man page
gagePathview Man page
gageSigGenes Man page
galp2gal Source code
gatkHaplotypeCaller Source code
getAvgProfileByOrientation Source code
getAvgTisReadStartProfiles Source code
getBSgenomes Source code
getBWAReference Man page Source code
getBamLocally Source code
getBamMultiMatching Man page Source code
getBinColors 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
getChildTerms 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
getExpressionGage Man page
getFeatureCounts Source code
getGOparents Man page Source code
getGeneIdExprLinks Man page Source code
getGeneMapping Man page Source code
getGeneSets Man page
getGeneTable Man page Source code
getGigabyteFree Man page Source code
getGigabyteTotal Source code
getGlobalDefaults Source code
getGoTermsAsTd Source code
getIgvGenome Man page Source code
getIgvLocusLink Man page Source code
getJunctionPlotsFromBam Man page Source code
getKallistoReference Man page Source code
getKeggId Man page
getOrganism,EzRef-method Man page
getPosErrorFromBam Man page Source code
getProfileMatrixForRanges Source code
getQualityMatrix Man page Source code
getQualityMatrix_old Source code
getRSEMReference Man page Source code
getRangeValues Man page Source code
getRangesCoverage Man page Source code
getReferenceFeaturesBed Man page Source code
getRleFromRanges Source code
getRpkm Man page Source code
getSTARReference Man page Source code
getSalmonReference Man page Source code
getSampleColors Man page Source code
getSampleLty Man page Source code
getSamplePch Man page Source code
getSignal Man page Source code
getSignificantCountsTable Man page Source code
getSignificantCountsTableSE Source code
getSignificantFoldChangeCountsTable Man page Source code
getSignificantFoldChangeCountsTableSE Source code
getSpeciesName Man page
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 Man page Source code
getTypeCoverageTable Man page 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
goClusterTable Man page
goClusterTableRmd Source code
goGroupBarPlot Source code
goStringsToList Man page Source code
goUpDownTables Source code
groupGff Man page Source code
hasFilesafeCharacters Man page Source code
hasGeneMapping Man page Source code
hasGoAnnotation Man page Source code
heatmapForPhyloseqPlot Source code
heatmapForPhylotseqPlotPheatmap Source code
heatmapPlate Man page Source code
imgLinks Man page Source code
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
lGetGlobalCountParam Man page Source code
lGetPyScriptPaths Man page
lastVal Man page Source code
listBiotypes Source code
loadCountDataset Man page Source code
loadSCCountDataset Man page Source code
logMessage Man page Source code
makeAlignmentCountBarPlot Man page Source code
makeCoordinate Man page Source code
makeCountResultSummary Source code
makeFeatAnnoEnsembl Source code
makeFragmentSizePlot Source code
makeIntervalList Source code
makeMinimalPairedEndReadDataset Man page Source code
makeMinimalSingleEndReadDataset Man page Source code
makeMultiMapping Man page Source code
makeResultFile Source code
makeScatterplot Source code
makeSignificantCounts Source code
makeSummarizedExperiment Source code
makeTagDirectory Source code
makeTailEffectPlots Source code
makeTestScatterData Source code
mapGoToSlim Source code
mergeBamAlignments Source code
mioString Man page Source code
mixedDatasetToMothur Source code
mkCurlQryString Man page Source code
modifyInput Man page Source code
multiGroupCountComparison Man page
myFisherTest Source code
ncpro Man page Source code
newWindowLink Man page Source code
normalized.distr Source code
onLoad Source code
openBsdocReport Man page Source code
otuSaturationPlot Source code Source code
otuSaturationTable Source code Source code
parseEnrichrLibNames Man page Source code
parseListOptions Source code
parseOptions Man page Source code
pcaForPhylotseqPlot Source code
phyloSeqCommunityComp Source code
phyloSeqDivPlotAndPercUnclassified Source code
phyloSeqOTU Source code Source code
phyloSeqOTUFromFile Source code
phyloSeqPreprocess Source code
phyloSeqSample Source code Source code
phyloSeqTaxa Source code Source code
phyloSeqTaxaFromFile Source code
phyloSeqToDeseq2_tableAndPlots Source code
plateStatistics Man page Source code
plotBamStat Man page
plotLocusAverageCoverageProfile Source code
plotLocusCoverageProfile Source code
plotPosSpecificErrorRate Man page Source code
plotQualityHeatmapGG2 Source code
plotQualityMatrixAsHeatmapGG2 Source code
plotReadCountToLibConc Source code
posSpecErrorBam Source code
posSpecErrorMDBam Source code
postProcessResults Man page Source code
prepareFilesLocallyForMothur Source code
prepareGOData Source code
prodigalFileReport Source code
readBam Source code
readGmt Man page
readNcProResult Man page Source code
readSCMM Man page Source code
removeReadsFromFastq Man page Source code
removeSuffix Man page Source code
remove_outliers Source code
revigoUpDownTables Source code
runCountSingleBam Man page Source code
runDeseq2 Man page Source code
runDeseq2MultiGroup Man page
runEdger Man page Source code
runEdgerGlmMultiGroup Man page
runEnrichr Man page Source code
runGageAnalysis Man page
runGatk Source code
runGatkPipeline Source code
runGfold Man page Source code
runGlm Man page Source code
runJunctionSeq Source code
runKraken Source code
runNgsCountQC Man page
runQoRTs Source code
runTEQC Man page Source code
separateGoIdsByOnto Man page Source code
setEnvironments Source code
setwdNew Man page Source code
seuratPreProcess Source code
shiftZeros Man page Source code
shrinkToRange Man page 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
summaryConfPlot Source code
summaryFamilyPlot Source code
summaryGOPlot Source code
summaryGcContPlot Source code
summaryMatchScorePlot Source code
summaryRBSMotifPlot Source code
summaryRBSSpacePlot Source code
summaryScorePlot Source code
tableFromSets Man page Source code
transcriptAnnoFromGtf Man page Source code
trimGRanges Man page Source code
trimTxGtf Source code
trimWhiteSpace Man page Source code
twoGroupCountComparison Man page Source code
twoGrouplsRoast 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
waitUntilFileExists Source code
writeAnnotationFromGtf Man page Source code
writeCountFilesToMeta Man page Source code
writeDEXSeqReport Man page Source code
writeErrorReport Man page Source code
writeGageResults Man page
writeIgvJnlp Man page Source code
writeIgvSession Man page Source code
writeIgvSessionLink Man page Source code
writeJavaScriptIgvStarter Man page
writeNgsMultiGroupReport Man page
writeOTUgzFileForVamps Source code
writePresplicedGtf Man page Source code
writeSCMM Man page Source code
zipFile Man page Source code
zipWorkingDir Man page Source code
uzh/ezRun documentation built on Dec. 9, 2018, 1:20 p.m.