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

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Documentation for package ‘RankMap’ version 0.99.1

• 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