Package index • RIRA

All functions

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

PredictTcellActivation(): Predicts T cell activation using sPLS derived components and a trained logistic model on transformed variates

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 probabilities.

ScoreUsingSavedComponent(): ScoreUsingSavedComponent

SetSeed(): Set random seed

TrainCellTypist(): Train Celltypist

TrainModel(): Creates a binary classifier to classify cells within a Seurat object

TrainModelsFromSeurat(): Wrapper function for TrainModel to train a suite of binary classifiers for each cell type present in the data