API for RamsinghLab/arkas_staging
A package that complements Kallisto for quick, informative *seq analysis
| Global functions | |
|---|---|
| .checkForAnnotation | Source code |
| .convertEntrezID | Source code |
| .extractRuninfo | Source code |
| .extractTranscriptomeFromCall | Source code |
| .findMart | Source code |
| .findPairings | Man page Source code |
| .formatLimmaWithMeta | Source code |
| .getIndexName | Source code |
| .getIndexPath | Source code |
| .tpmBySample | Man page Source code |
| ERCC_annotated | Man page Man page |
| KEtoSE | Man page Source code |
| KallistoExperiment | Man page Source code |
| KallistoExperiment-class | Man page Man page Man page Man page Man page Man page |
| KallistoExperiment-method | Man page Man page Man page Man page Man page |
| SEtoKE | Man page Source code |
| annotateFeatures | Man page Source code |
| calcTpm | Man page Source code |
| collapseBundles | Man page Source code |
| collapseByTss | Man page Source code |
| collapseTpm | Man page Source code |
| collapseTranscripts | Man page Source code |
| counts,KallistoExperiment-method | Man page |
| crossModels | Man page Source code |
| dumpToBigWig | Man page Source code |
| eff_length | Man page |
| eff_length,KallistoExperiment-method | Man page |
| extractIndexName | Man page Source code |
| fastqFileUploadToBaseSpace | Man page Source code |
| fetchAppSession | Man page Source code |
| fetchKallisto | Man page Source code |
| fitBundles | Man page Source code |
| fitRepeats | Man page Source code |
| fitTranscripts | Man page Source code |
| geneWiseAnalysis | Man page Source code |
| getKallistoVersion | Man page Source code |
| indexKallisto | Man page Source code |
| kallistoVersion | Man page |
| kallistoVersion,KallistoExperiment-method | Man page |
| mabDev | Man page |
| mabDev,KallistoExperiment-method | Man page |
| mergeKallisto | Man page Source code |
| pData,KallistoExperiment-method | Man page |
| pData<-,KallistoExperiment,DataFrame-method | Man page |
| pairFastqFiles | Man page Source code |
| parseFastqNames | Man page Source code |
| remapSymbols | Man page Source code |
| repeatWiseAnalysis | Man page Source code |
| rpkmToTpm | Man page Source code |
| runKallisto | Man page Source code |
| ruvNormalization | Man page Source code |
| showTnxBundles | Man page Source code |
| sraFastqHeaderToIlluminaStandard | Man page Source code |
| tpm | Man page |
| tpm,KallistoExperiment-method | Man page |
| transcriptWiseAnalysis | Man page Source code |
| transcriptomes | Man page |
| transcriptomes,KallistoExperiment-method | Man page |
| unannotatedTranscript | Man page |
