API for recoup
An R package for the creation of complex genomic profile plots
| Global functions | |
|---|---|
| ..getAllUcsc | Source code |
| ..getUcscSqlite | Source code |
| .annotationExists | Source code |
| .annotationTypeFromInputArgs | Source code |
| .browseContent | Source code |
| .browseUserContent | Source code |
| .chromInfoFromBAM | Source code |
| .chromInfoFromSeqinfo | Source code |
| .chromInfoToSeqInfoDf | Source code |
| .dropAnnotation | 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 |
| .initTables | Source code |
| .insertContent | Source code |
| .installedVersions | Source code |
| .loadAnnotationOnTheFly | Source code |
| .loadPrebuiltAnnotation | Source code |
| .localTblDef | Source code |
| .makeAnnotationQuerySet | Source code |
| .makeGeneExonFromTxDb | Source code |
| .makeGeneGeneFromTxDb | Source code |
| .makeGeneUtrFromTxDb | Source code |
| .makeIdMap | Source code |
| .makeSumGeneExonFromTxDb | Source code |
| .makeSumGeneUtrFromTxDb | Source code |
| .myGetBM | Source code |
| .nameAnnotationFromMetaType | Source code |
| .subsetGRangesByBamHeader | Source code |
| .subsetGRangesByChrs | Source code |
| .userOrg | Source code |
| .userRefdb | Source code |
| .validateDbCon | Source code |
| .validateEnsemblVersions | Source code |
| annotationFromCustomGtf | Source code |
| applySelectors | Source code |
| areColors | Source code |
| baseCoverageMatrix | Source code |
| baseCoverageMatrixOld | Source code |
| binCoverageMatrix | Source code |
| buildAnnotationDatabase | Man page Source code |
| buildAnnotationStore | Man page Source code |
| buildCustomAnnotation | Man page Source code |
| calcCoverage | Man page Source code |
| calcLinearFactors | Source code |
| checkFileArgs | Source code |
| checkInput | Source code |
| checkMainArgs | Source code |
| checkNumArgs | Source code |
| checkTextArgs | Source code |
| checkUcscToEnsembl | Source code |
| cleanRanges | Source code |
| cmclapply | Source code |
| contVector | Source code |
| correctTranscripts | Source code |
| covLengthsEqual | Source code |
| coverageFromBam | Source code |
| coverageFromBigWig | Source code |
| coverageFromRanges | Source code |
| coverageRef | Man page Source code |
| coverageRnaRef | Man page Source code |
| decideChanges | Source code |
| fixedRangedBinSizes | Source code |
| flankFirstLast | Source code |
| getAnnotation | Man page Source code |
| getArg | Source code |
| getBiotypes | Man page Source code |
| getBsOrganism | Source code |
| getChromInfo | Source code |
| getDataset | Source code |
| getDefaultListArgs | Source code |
| getEnsemblAnnotation | Source code |
| getExonAttributes | Source code |
| getFlankingRanges | Source code |
| getGcContent | Source code |
| getGeneAttributes | Source code |
| getHost | Source code |
| getInstalledAnnotations | Man page Source code |
| getMainRanges | Source code |
| getMainRnaRanges | Source code |
| getRegionalRanges | Source code |
| getSeqInfo | Source code |
| getSupportedOrganisms | Source code |
| getSupportedRefDbs | Source code |
| getSupportedUcscDbs | Source code |
| getTranscriptAttributes | Source code |
| getTranscriptUtrAttributes | 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 |
| getr | Man page Source code |
| importCustomAnnotation | Man page Source code |
| importCustomGtf | Source code |
| imputeZero | Source code |
| initDatabase | Source code |
| interpolateSignal | Source code |
| kmeansDesign | Man page Source code |
| lazyRangesCoverage | Source code |
| lazyRangesListCoverage | Source code |
| loadAnnotation | Man page Source code |
| loadBsGenome | Source code |
| mergeRuns | Man page Source code |
| parseCustomGtf | Source code |
| prepareBam | Source code |
| preprocessRanges | Man page Source code |
| profileMatrix | Man page Source code |
| profileMatrixSample | Source code |
| readBam | Source code |
| readBamIntervals | Source code |
| readBed | Source code |
| readConfig | Source code |
| readRanges | Source code |
| recoup | Man page Source code |
| recoup-defunct | Man page |
| recoup-deprecated | Man page |
| recoupCorrelation | Man page |
| recoupHeatmap | Man page |
| recoupPlot | Man page Source code |
| recoupProfile | Man page Source code |
| recoup_test_data | Man page |
| reduceExons | Source code |
| reduceTranscripts | Source code |
| reduceTranscriptsUtr | Source code |
| removeData | Man page Source code |
| reorderClusters | Source code |
| resizeRanges | Source code |
| rpMatrix | Man page Source code |
| rpMatrixSample | Source code |
| setArg | Source code |
| setr | Man page Source code |
| sliceObj | Man page Source code |
| splitRanges | Source code |
| splitRangesList | Source code |
| splitVector | Source code |
| ssCI | Source code |
| test.design | Man page |
| test.exons | Man page |
| test.genome | Man page |
| test.input | Man page |
| tileRanges | Source code |
| toOutput | Source code |
| ucscToEnsembl | Source code |
| validateListArgs | Source code |
| validateOrganismArg | Source code |
| variableRangedBinSizes | Source code |
