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

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Documentation for package ‘AUCell’ version 1.26.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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