Man pages for bimberlabinternal/RIRA_classification
A package for the Rhesus Immune Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells
| AssignCellType | Assigns celltype label based on probabilities in the metadata |
| CalculateUCellScores | CalculateUCellScores |
| Classify_ImmuneCells | Classify Bulk Immune cells |
| Classify_Myeloid | Classify T/NK |
| Classify_TNK | Classify T/NK |
| DownloadFromGEO | Download RIRA data from GEO |
| ExpandGeneList | ExpandGeneList |
| ExtractGeneWeights | ExtractGeneWeights |
| FilterDisallowedClasses | Filter Disallowed Classes |
| GetAvailableScGates | GetAvailableScGates |
| GetGeneSet | GetGeneSet |
| GetMMul10IgGenes | GetMMul10IgGenes |
| GetMMul10TcrGenes | GetMMul10TcrGenes |
| GetScGateModel | GetScGateModel |
| GetSeed | Get random seed |
| InterpretModels | Interprets the feature importance of each model |
| ListGeneSets | ListGeneSets |
| MakePhenotypingDotPlot | MakePhenotypingDotPlot |
| PlotImmuneMarkers | PlotImmuneMarkers |
| PlotMarkerSeries | PlotMarkerSeries |
| PlotUcellCorrelation | PlotUcellCorrelation |
| PredictCellTypeProbability | Applies trained models to get celltype probabilities |
| RunCellTypist | Run Celltypist |
| RunScGate | Run scGate |
| RunScGateForModels | Run scGate for models |
| RunScGateWithDefaultModels | Run scGate With DefaultModels |
| RunScGateWithRhesusModels | Run scGate using Rhesus macaque models |
| ScoreCellsWithSavedModel | Applies a trained binary classifier to get per-cell... |
| ScoreUsingSavedComponent | ScoreUsingSavedComponent |
| SetSeed | Set random seed |
| TrainCellTypist | Train Celltypist |
| TrainModel | Creates a binary classifier to classify cells within a Seurat... |
| TrainModelsFromSeurat | Wrapper function for TrainModel to train a suite of binary... |
