API for metaseqR2
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
| Global functions | |
|---|---|
| ..getAllUcsc | Source code |
| ..getUcscSqlite | Source code |
| .adjustOrDropSeqlevels | Source code |
| .adjustSeqlevelsStyle | Source code |
| .annotationExists | Source code |
| .annotationTypeFromInputArgs | Source code |
| .backPreprocessAnnotation | Source code |
| .backwardsCompatibility | Source code |
| .backwardsConvertArgs | Source code |
| .backwardsMapOld2New | Source code |
| .browseContent | Source code |
| .browseUserContent | Source code |
| .calcFactorQuantile | Source code |
| .calcFactorWeighted | Source code |
| .calcNormFactors | Source code |
| .chromInfoFromBAM | Source code |
| .chromInfoFromSeqinfo | Source code |
| .chromInfoToSeqInfoDf | Source code |
| .chromInfoWrapperGID | Source code |
| .convertSam | Source code |
| .createDexiePlotDb | Source code |
| .createR2CExport | Source code |
| .createSqlPlotDb | Source code |
| .createStrandedSignalTracks | Source code |
| .createTrackHub | Source code |
| .createUnstrandedSignalTracks | Source code |
| .dbImportPlot | Source code |
| .deprecatedWarning | Source code |
| .downloadJsLibs | Source code |
| .dropAnnotation | Source code |
| .excludeSamplesFromList | Source code |
| .externalGtfToBigBed | Source code |
| .formatForReport | Source code |
| .getBackwardsValidArgs | Source code |
| .getColorScheme | Source code |
| .getColors | Source code |
| .getExonAttributes | Source code |
| .getGeneAttributes | Source code |
| .getGroupColorScheme | Source code |
| .getNegBaseColors | Source code |
| .getPosBaseColors | Source code |
| .getStatMap | Source code |
| .getTranscriptAttributes | Source code |
| .getTranscriptExonAttributes | Source code |
| .getTranscriptUtrAttributes | Source code |
| .getUcscCredentials | Source code |
| .getUcscQueryRefseqExon | Source code |
| .getUcscQueryRefseqGene | Source code |
| .getUcscQueryRefseqTranscript | Source code |
| .getUcscQueryUcscExon | Source code |
| .getUcscQueryUcscGene | Source code |
| .getUcscQueryUcscTranscript | Source code |
| .getUcscTabledefRefseq | Source code |
| .getUcscTabledefUcsc | Source code |
| .getValidArgs | Source code |
| .initReportDbTables | Source code |
| .initTables | Source code |
| .insertContent | Source code |
| .installedVersions | Source code |
| .loadAnnotationOnTheFly | Source code |
| .loadPrebuiltAnnotation | Source code |
| .localTblDef | Source code |
| .makeAnnotationQuerySet | Source code |
| .makeExonExonFromTxDb | Source code |
| .makeGeneExonFromTxDb | Source code |
| .makeGeneGeneFromTxDb | Source code |
| .makeGeneUtrFromTxDb | Source code |
| .makeHtmlBody | Source code |
| .makeHtmlCells | Source code |
| .makeHtmlHeader | Source code |
| .makeHtmlRows | Source code |
| .makeHtmlTable | Source code |
| .makeIdMap | Source code |
| .makeReportEnv | Source code |
| .makeSumGeneExonFromTxDb | Source code |
| .makeSumGeneUtrFromTxDb | Source code |
| .makeSumTranscriptGeneFromTxDb | Source code |
| .makeSumTranscriptUtrFromTxDb | Source code |
| .makeTrackhubEntrypoint | Source code |
| .makeTrackhubGenomesFile | Source code |
| .makeTrackhubGroupsFile | Source code |
| .makeTrackhubMultiwig | Source code |
| .makeTrackhubSinglewig | Source code |
| .makeTranscriptExonFromTxDb | Source code |
| .makeTranscriptGeneFromTxDb | Source code |
| .makeTranscriptUtrFromTxDb | Source code |
| .myCreateFilterXMLchunk | Source code |
| .myGenerateFilterXML | Source code |
| .myGetBM | Source code |
| .myMartCheck | Source code |
| .mySetResultColNames | Source code |
| .mySplitValues | Source code |
| .nameAnnotationFromMetaType | Source code |
| .readTabTargets | Source code |
| .readYamlTargets | Source code |
| .reduceExonsOld | Source code |
| .reduceGeneData | Source code |
| .reduceTranscriptsOld | Source code |
| .reduceTranscriptsUtrOld | Source code |
| .reportDbTblDef | Source code |
| .unquote_js_fun | Source code |
| .userOrg | Source code |
| .userRefdb | Source code |
| .validateDbCon | Source code |
| .validateEnsemblVersions | Source code |
| .writeTargets | Source code |
| .zeroFix | Source code |
| ARSyNcomponents | Source code |
| ARSyNmodel | Source code |
| ARSyNseq | Source code |
| ASCA.1f | Source code |
| ASCA.2f | Source code |
| ASCA.3f | Source code |
| ASCAfun.triple | Source code |
| ASCAfun1 | Source code |
| ASCAfun2 | Source code |
| CV | Source code |
| DE.plot | Source code |
| PCA.GENES | Source code |
| addData | Source code |
| adjustScvForBias | Source code |
| allMDbio | Source code |
| annotationFromCustomGtf | Source code |
| asClassVector | Source code |
| biasPlotToJSON | Source code |
| bioDetectionToJSON | Source code |
| bioSaturationToJSON | Source code |
| biodetection.dat | Source code |
| biodetection.plot | Source code |
| biodistToJSON | Source code |
| boxplotToJSON | Source code |
| buildAnnotationDatabase | Man page Source code |
| buildCustomAnnotation | Man page Source code |
| buildExport | Source code |
| calcF1Score | Source code |
| calcOtr | Source code |
| checkContrastFormat | Source code |
| checkFileArgs | Source code |
| checkGraphicsFile | Source code |
| checkGraphicsType | Source code |
| checkLibsize | Source code |
| checkMainArgs | Source code |
| checkNumArgs | Source code |
| checkPackages | Source code |
| checkTextArgs | Source code |
| checkUcscToEnsembl | Source code |
| cmclapply | Source code |
| combineBonferroni | Man page Source code |
| combineHarmonic | Man page Source code |
| combineMaxp | Man page Source code |
| combineMinp | Man page Source code |
| combineSimes | Man page Source code |
| combineWeight | Man page Source code |
| constructGeneModel | Source code |
| correctTranscripts | Source code |
| countsBioToJSON | Source code |
| countsbio.plot | Source code |
| createSignalTracks | Man page Source code |
| dat | Source code |
| dereguloToJSON | Source code |
| diagplotAvgFtd | Man page Source code |
| diagplotBoxplot | Man page Source code |
| diagplotCor | Man page Source code |
| diagplotDeHeatmap | Man page Source code |
| diagplotDeregulogram | Source code |
| diagplotEdaseq | Man page Source code |
| diagplotFiltered | Man page Source code |
| diagplotFtd | Man page Source code |
| diagplotMa | Source code |
| diagplotMds | Man page Source code |
| diagplotNoiseq | Man page Source code |
| diagplotNoiseqSaturation | Source code |
| diagplotPairs | Man page Source code |
| diagplotRoc | Man page Source code |
| diagplotVenn | Man page Source code |
| diagplotVolcano | Man page Source code |
| disp | Source code |
| downsampleCounts | Man page Source code |
| elap2human | Source code |
| estimateAndFitDispersionsFromBaseMeansAndVariances | Source code |
| estimateAndFitDispersionsWithCoxReid | Source code |
| estimateAufcWeights | Man page Source code |
| estimateSimParams | Man page Source code |
| estimateSizeFactorsForMatrix | Source code |
| exampleCountData | Source code |
| filterExons | Source code |
| filterGenes | Source code |
| filterHigh | Source code |
| filterLow | Source code |
| filtered.data | Source code |
| filteredToJSON | Source code |
| fisherMethod | Source code |
| fisherMethodPerm | Source code |
| fisherSum | Source code |
| fitInfo | Source code |
| fitNbinomGLMs | Source code |
| fitNbinomGLMsForMatrix | Source code |
| getAltHost | Source code |
| getAnnotation | Man page Source code |
| getArg | Source code |
| getBaseMeansAndPooledVariances | Source code |
| getBaseMeansAndVariances | Source code |
| getBiotypes | Source code |
| getBsOrganism | Source code |
| getChromInfo | Source code |
| getDataset | Source code |
| getDefaults | Man page Source code |
| getEnsemblAnnotation | Source code |
| getGcContent | Source code |
| getHost | Source code |
| getInstalledAnnotations | Man page Source code |
| getPresetOpts | Source code |
| getSeqInfo | Source code |
| getStrictBiofilter | Source code |
| getSupportedOrganisms | Source code |
| getSupportedRefDbs | Source code |
| getSupportedUcscDbs | Source code |
| getUcscAnnotation | Source code |
| getUcscDbl | Source code |
| getUcscOrganism | Source code |
| getUcscQuery | Source code |
| getUcscTableNameUtr | Source code |
| getUcscTabledef | Source code |
| getUcscTblTpl | Source code |
| getUcscToEnsembl | Source code |
| getUcscUtr | Source code |
| getUserAnnotations | Source code |
| getValidChrs | Source code |
| getValidChrsWithMit | Source code |
| getVarianceStabilizedData | Source code |
| getWeights | Man page Source code |
| graphicsClose | Source code |
| graphicsOpen | Source code |
| hg19pvalues | Man page |
| importCustomAnnotation | Man page Source code |
| importCustomGtf | Source code |
| initDatabase | Source code |
| int.mult | Source code |
| libsizeListMm9 | Man page |
| loadAnnotation | Man page Source code |
| loadBsGenome | Source code |
| log2disp | Source code |
| logscaling | Source code |
| maStatToJSON | Source code |
| make.ASCA.design | Source code |
| makeA | Source code |
| makeAvgExpression | Source code |
| makeContrastList | Source code |
| makeExportList | Source code |
| makeFoldChange | Source code |
| makeGrid | Source code |
| makeHighchartsPoints | Source code |
| makeHighchartsVennSets | Source code |
| makeJVennFoldData | Source code |
| makeJVennStatData | Source code |
| makeMatrix | Source code |
| makeMoreVennPairs | Source code |
| makePathStruct | Source code |
| makePermutation | Source code |
| makeProjectPath | Source code |
| makeReportMessages | Source code |
| makeSampleList | Source code |
| makeSimDataSd | Man page Source code |
| makeSimDataTcc | Man page Source code |
| makeStat | Source code |
| makeTransformation | Source code |
| makeVennAreas | Source code |
| makeVennColorscheme | Source code |
| makeVennCounts | Source code |
| makeVennPairs | Source code |
| mdsToJSON | Source code |
| metaPerm | Source code |
| metaTest | Man page Source code |
| metaWorker | Source code |
| metaseqr2 | Man page Source code |
| metaseqrPlot | Man page Source code |
| mlfo | Source code |
| mm9GeneCounts | Man page |
| modelMatrixToConditionFactor | Source code |
| mypretty | Source code |
| nat2log | Source code |
| nbinomGLMTest | Source code |
| nbinomTest | Source code |
| nbinomTestForMatrices | Source code |
| nbkd.sf | Source code |
| newCountDataSet | Source code |
| normalizeAbsseq | Man page Source code |
| normalizeDeseq | Man page Source code |
| normalizeDeseq2 | Man page Source code |
| normalizeDss | Man page Source code |
| normalizeEdaseq | Man page Source code |
| normalizeEdger | Man page Source code |
| normalizeNbpseq | Man page Source code |
| normalizeNoiseq | Man page Source code |
| parametricDispersionFit | Source code |
| parseCustomGtf | Source code |
| plot.y2 | Source code |
| prepareScvBiasCorrectionFits | Source code |
| profileLogLikelihood | Source code |
| ranking | Source code |
| read2count | Man page Source code |
| readData | Source code |
| readNoiseToJSON | Source code |
| readTargets | Man page Source code |
| reduceExons | Source code |
| reduceTranscripts | Source code |
| reduceTranscriptsExons | Source code |
| reduceTranscriptsUtr | Source code |
| rnacompToJSON | Source code |
| safepredict | Source code |
| sampleListMm9 | Man page |
| scatterToJSON | Source code |
| setArg | Source code |
| sim.samples | Source code |
| statAbsseq | Man page Source code |
| statBayseq | Man page Source code |
| statDeseq | Man page Source code |
| statDeseq2 | Man page Source code |
| statDss | Man page Source code |
| statEdger | Man page Source code |
| statLimma | Man page Source code |
| statNbpseq | Man page Source code |
| statNoiseq | Man page Source code |
| stopwrap | Source code |
| ucscToEnsembl | Source code |
| validateAlgArgs | Source code |
| validateListArgs | Source code |
| volcanoToJSON | Source code |
| warnwrap | Source code |
| wpAdjust | Source code |
