API for dyohanne/RepAn
Differential abundance Analysis for deep sequenced immune repertoire (Repseq) datasets
| Global functions | |
|---|---|
| CDRepseqObj | Man page |
| CountkmerFrequency | Man page Source code |
| TopDAClonotypes | Man page Source code |
| addItemToObject | Man page Source code |
| compareAbundanceInPairedSamples | Source code |
| compareAbundanceInPairedSamplesForRanking | Man page |
| compareAbundanceInSamplesForRanking | Source code |
| compareAbundanceInTwoSamplesForShared | Source code |
| compareClusterAbundancesPaired | Man page Source code |
| compareClusterAbundancesUnPaired | Man page Source code |
| compareUsageInTwoSamples | Source code |
| compareUsageProportions | Source code |
| compareUsageProportionsPaired | Source code |
| computeVgeneEnrichement | Man page Source code |
| cosineDist | Man page Source code |
| createDecoyCDR3s_V1 | Source code |
| createDecoyCDR3s_V2 | Man page Source code |
| determineWeight | Man page Source code |
| extractCDR3 | Source code |
| extractDASubRepertoire | Man page Source code |
| extractSubRepertoire | Man page Source code |
| findDAClonotypesInDACluster | Man page |
| findDAClusters | Man page Source code |
| findOptimalClusters | Man page Source code |
| findOptimalK | Man page Source code |
| getAbundantClonotypesbynumber | Source code |
| getAbundantClonotypesbyperc | Source code |
| getAggregateCount | Source code |
| getAllJgenes | Source code |
| getAllVJgenes | Source code |
| getAllVfamilies | Source code |
| getAllVgenes | Source code |
| getCenters | Man page Source code |
| getClonalKmerNtFrequencies | Source code |
| getClusterAbundancesTable | Man page Source code |
| getClusterFoldChanges | Man page Source code |
| getClusterLables | Man page Source code |
| getClusterMatches | Man page Source code |
| getDefined | Man page Source code |
| getHasStop | Man page Source code |
| getKmerFrequency | Man page Source code |
| getKmerNtFrequencies | Source code |
| getKmerNtFrequenciesVJ | Source code |
| getMatchingCluster | Man page Source code |
| getOutOfFrame | Man page Source code |
| getPCAfordata | Source code |
| getPCAfordata1 | Source code |
| getPCAfordata2 | Source code |
| getPCAfordata3 | Source code |
| getPCAfordata4 | Source code |
| getPooledSamples | Man page Source code |
| getProductive | Man page Source code |
| getUniqueJgenes | Source code |
| getUniqueVfamilies | Source code |
| getUniqueVfamilies_PBMC | Source code |
| getUniqueVgenes | Source code |
| getUnproductive | Man page Source code |
| getVgeneCloneCountMatrix | Source code |
| getVgeneCloneCountMatrixUnprod | Source code |
| getVgeneCloneCountPMatrix | Source code |
| getVgeneCloneCountPMatrixUnprod | Source code |
| getVgeneReadCountMatrix | Source code |
| getVgeneReadCountMatrixUnprod | Source code |
| getVgeneReadCountPMatrix | Source code |
| getVgeneReadCountPMatrixUnprod | Source code |
| getVjCloneCountMatrix | Source code |
| getVjCloneCountMatrixUnprod | Source code |
| getVjCloneCountPMatrix | Source code |
| getVjCloneCountPMatrixUnprod | Source code |
| getVjReadCountMatrix | Source code |
| getVjReadCountMatrixUnprod | Source code |
| getVjReadCountPMatrix | Source code |
| getVjReadCountPMatrixUnprod | Source code |
| item.exists | Man page Source code |
| loadBioconductorPacks | Man page Source code |
| loadPacks | Man page Source code |
| normalizeSamples | Source code |
| overLappingClonotypes | Source code |
| overLappingClonotypes2 | Source code |
| overLappingClonotypesAA | Source code |
| overLappingClonotypesByChoice | Source code |
| overLappingClonotypesHasStop | Source code |
| readMiXCR | Source code |
| readSample | Man page Source code |
| readSampleV2 | Man page Source code |
| renameCopyTOCount | Source code |
| resampleReferenceSamples | Man page Source code |
| runDaAnalysis | Man page Source code |
| sampleFromPooled | Man page Source code |
| sampleWithFeatuersFromPooled | Man page Source code |
| scaleSamples | Man page Source code |
| setUp | Man page Source code |
| shannonEntropy | Man page Source code |
