API for RGLab/RNASeqPipelineR
Construct Standardized pipelines for processing RNASeq data
| Global functions | |
|---|---|
| .collectFastqcFiles | Source code |
| .createGenomeDict | Source code |
| .createSampleFile | Source code |
| AlignmentSTAR | Man page Source code |
| MiTCR | Man page Source code |
| QualityControl | Man page Source code |
| RNASeqPipeline | Man page |
| RNASeqPipeline-package | Man page |
| RSEMAssembleExpressionMatrix | Man page Source code |
| RSEMCalculateExpression | Man page Source code |
| RSEMSummarizeMapping | Man page Source code |
| SRAOverview | Man page Source code |
| annotateSRA | Man page Source code |
| annotateUCSC | Man page Source code |
| annotationsFromSRX | Man page Source code |
| assignConfig | Man page Source code |
| buildGenomeIndexSTAR | Man page |
| buildGenomeIndexSTAR2 | Man page |
| buildReference | Man page Source code |
| concatenateFastq | Man page Source code |
| configure_project | Man page Source code |
| convertSRAtoFastQ | Man page Source code |
| createProject | Man page Source code |
| detectAspera | Man page Source code |
| devel_truncateData | Man page Source code |
| downloadSRA | Man page Source code |
| getAndConnectSRAdb | Man page Source code |
| getConfig | Man page Source code |
| getConfigDir | Man page Source code |
| getConfigFile | Man page Source code |
| getDataFromSRX | Man page Source code |
| getDir | Man page Source code |
| getExpressionSet | Man page Source code |
| kallistoAlign | Man page Source code |
| kallistoAssembleOutput | Man page Source code |
| kallistoAssembleQC | Man page Source code |
| kallistoBuildTranscriptIndex | Man page Source code |
| kallistoReadQC | Man page Source code |
| loadImmportTables | Man page Source code |
| loadProject | Man page Source code |
| mergeData | Man page Source code |
| pear | Man page Source code |
| pipelineReport | Man page Source code |
| qualityRNASeQC | Man page Source code |
| readConfig | Man page Source code |
| runFastQC | Man page Source code |
| saveConfig | Man page Source code |
| sequenceAlignmentTopHat | Man page Source code |
| setGenomeReference | Man page Source code |
| stripExtension | Source code |
| sumDuplicates | Man page Source code |
| summarizeDuplication | Man page Source code |
| summarizeFastQC | Man page Source code |
