# Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics

## Documentation for package ‘RankMap’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

computeRankedMatrix | Compute Ranked Gene Expression Matrix
evaluatePredictionPerformance | Evaluate Prediction Accuracy and Confusion by Cell Type
extractData | Extract Expression Matrix from Seurat, SummarizedExperiment, or Matrix
factorSorted | Order factor levels by frequency
filterLowConfidenceCells | Tag Low-Confidence Predictions and Add Status Column
maskTopKGenes | Mask Non-Top-K Genes in Each Cell or Spot
optimizeConfidenceThreshold | Optimize Confidence Threshold for Cell Type Prediction
predictRankModel | Predict Cell Types, Probabilities, or Confidence Scores
RankMap | RankMap: Train and Predict Cell Types Using Top-Ranked Genes
sampleCellsByType | Sample Cells by Cell Type with Minimum Representation
trainRankModel | Train Multinomial Rank-Based Model