# AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

## Documentation for package ‘AUCell’ version 1.34.0

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

## Help Pages

aucellResults | Wrapper to the matrix that stores the AUC or the cell rankings.
aucellResults-class | Wrapper to the matrix that stores the AUC or the cell rankings.
AUCell_assignCells | AUCell_assignCells
AUCell_buildRankings | Build gene expression rankings for each cell
AUCell_buildRankings-method | Build gene expression rankings for each cell
AUCell_calcAUC | Calculate AUC
AUCell_calcAUC-method | Calculate AUC
AUCell_exploreThresholds | AUCell_exploreThresholds
AUCell_plotHist | Plot AUC histogram
AUCell_plotTSNE | Plot
AUCell_run | Run AUCell
AUCell_run-method | Run AUCell
cbind | Wrapper to the matrix that stores the AUC or the cell rankings.
cbind-method | Wrapper to the matrix that stores the AUC or the cell rankings.
getAssignments | AUCell_exploreThresholds
getAUC | Wrapper to the matrix that stores the AUC or the cell rankings.
getAUC-method | Wrapper to the matrix that stores the AUC or the cell rankings.
getRanking | Wrapper to the matrix that stores the AUC or the cell rankings.
getRanking-method | Wrapper to the matrix that stores the AUC or the cell rankings.
getSetNames | Get gene set name (excluding number of genes/regions after space)
getThresholdSelected | AUCell_exploreThresholds
nGenes | GeneSet methods
nGenes-method | GeneSet methods
orderAUC | orderAUC
plotEmb_rgb | plotEmb_rgb
plotGeneCount | plotGeneCount
plotTsne_cellProps | plotTsne_cellProps
rbind | Wrapper to the matrix that stores the AUC or the cell rankings.
rbind-method | Wrapper to the matrix that stores the AUC or the cell rankings.
setGeneSetNames | GeneSet methods
setGeneSetNames-method | GeneSet methods
show | Wrapper to the matrix that stores the AUC or the cell rankings.
show-method | Wrapper to the matrix that stores the AUC or the cell rankings.
subsetGeneSets | GeneSet methods
subsetGeneSets-method | GeneSet methods
updateAucellResults | Update AUCell results