API for khodosevichlab/CellAnnotatoR
Automated marker-based cell type annotation
| Global functions | |
|---|---|
| aggregateScoreChangePerGene | Man page Source code |
| annotationFromScores | Source code |
| arrangePlots | Man page Source code |
| assignCellsByScores | Man page |
| classificationTreeToDf | Man page Source code |
| createClassificationTree | Man page |
| deriveHierarchy | Man page |
| diffuseGraph | Man page Source code |
| diffuseScorePerType | Man page Source code |
| estimateDNegativeScores | Source code |
| estimateNewNegativeScores | Source code |
| estimatePariwiseNegativeScoreChange | Source code |
| expandAnnotationToClusters | Source code |
| extractCellTypeProbs | Man page |
| extractMarkersFromSubtypes | Man page Source code |
| getAnnotationConfidence | Source code |
| getAnnotationPerParent | Man page Source code |
| getCellTypeScoreInfo | Man page |
| getClassificationData | Man page |
| getMarkerScoreInfo | Man page |
| getMarkerScoresPerCellType | Man page |
| getTopNegativeGenes | Man page |
| hierarchyToClassificationTree | Man page |
| markerListToMarkup | Man page |
| mergeAnnotationByLevels | Man page |
| mergeAnnotationToLevel | Man page Source code |
| mergeScoreInfos | Man page |
| mergeScores | Man page |
| normalizeTCWithFeatures | Man page |
| normalizeTfIdfWithFeatures | Man page |
| parseMarkerFile | Man page |
| plapply | Man page Source code |
| plotAnnotationByLevels | Source code |
| plotAssignmentScores | Man page Source code |
| plotConfidenceByLevels | Source code |
| plotGeneExpression | Man page |
| plotMarkerListViolinMap | Man page |
| plotOneUncertaintyPerClust | Man page |
| plotSubtypeMarkers | Man page Source code |
| plotTypeHierarchy | Source code |
| plotTypeMarkers | Man page Source code |
| plotUncertaintyPerCell | Man page Source code |
| plotUncertaintyPerClust | Man page |
| prepareDeInfo | Man page |
| scoreCellUncertaintyPerLevel | Man page |
| scoreClusterUncertaintyPerLevel | Man page |
| scorePerCellUncertainty | Man page Source code |
| selectMarkersPerType | Man page |
| sparseColMax | Source code |
| sparseRowMax | Source code |
| unifyGeneIds | Source code |
