Man pages for khodosevichlab/CellAnnotatoR
Automated marker-based cell type annotation
| aggregateScoreChangePerGene | Aggregate Score Change per Gene |
| arrangePlots | Arrange Plots |
| assignCellsByScores | Assign Cells By Scores |
| classificationTreeToDf | Classification Tree to DataFrame |
| createClassificationTree | Create Classification Tree |
| deriveHierarchy | Derive Hierarchy |
| diffuseGraph | Diffuse Graph |
| diffuseScorePerType | Diffuse Score per Type |
| extractCellTypeProbs | Extract Cell Type Probabilities |
| extractMarkersFromSubtypes | Extract Markers From Subtypes |
| getAnnotationPerParent | Get Annotation Per Parent |
| getCellTypeScoreInfo | Get Cell Type Score Info |
| getClassificationData | Get Classification data |
| getMarkerScoreInfo | Get Marker Score Info |
| getMarkerScoresPerCellType | Return initial scores of each cell type for each cell |
| getTopNegativeGenes | Get Top Negative Genes |
| hierarchyToClassificationTree | Hierarchy to Classification Tree |
| markerListToMarkup | Marker List to Markup |
| mergeAnnotationByLevels | Merge Annotation By Levels |
| mergeAnnotationToLevel | Merge Annotation to Level |
| mergeScoreInfos | Merge Score Infos |
| mergeScores | Merge Scores |
| normalizeTCWithFeatures | Normalize Total Count with Features |
| normalizeTfIdfWithFeatures | Normalize TF-IDF with Features |
| parseMarkerFile | Parse Marker File |
| plapply | Parallel Lapply |
| plotAssignmentScores | Plot Assignment Scores |
| plotGeneExpression | Plot gene expression on cell embedding |
| plotMarkerListViolinMap | Plot expression violin map for given marker list |
| plotOneUncertaintyPerClust | Plot One Uncertainty per Cluster |
| plotSubtypeMarkers | Plot Subtype Markers |
| plotTypeMarkers | Plot Type Markers |
| plotUncertaintyPerCell | Uncertainty scatterplots per cell |
| plotUncertaintyPerClust | Uncertainty barplots per cluster |
| prepareDeInfo | Prepare DE Info |
| scoreCellUncertaintyPerLevel | Score Cell Uncertainty Per Level |
| scoreClusterUncertaintyPerLevel | Score Cluster Uncertainty Per Level |
| scorePerCellUncertainty | Score Per Cell Uncertainty |
| selectMarkersPerType | Select Markers per Type |
