Single cell replicability analysis

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Documentation for package ‘MetaNeighbor’ version 1.22.0

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

Help Pages

extendClusterSet	Extend cluster set to nearest neighbors on cluster graph.
extractMetaClusters	Extracts groups of reciprocal top hits from a 1-vs-best AUROC matrix.
getCellType	Return cell type from a label in format 'study_id|cell_type'
getStudyId	Return study ID from a label in format 'study_id|cell_type'
ggPlotHeatmap	Plots symmetric AUROC heatmap, clustering cell types by similarity.
GOhuman	GOhuman
GOmouse	GOmouse
makeClusterGraph	Convert AUROC matrix into a graph.
makeClusterName	Make cluster names in format 'study_id|cell_type'
mergeSCE	Merge multiple SingleCellExperiment objects.
MetaNeighbor	Runs MetaNeighbor
MetaNeighborUS	Runs unsupervised version of MetaNeighbor
mn_data	mn_data
neighborVoting	Runs the neighbor voting algorithm.
orderCellTypes	Order cell types based on AUROC similarity matrix.
plotBPlot	Plot Bean Plot, showing how replicability of cell types depends on gene sets.
plotClusterGraph	Plot cluster graph generated with makeClusterGraph.
plotDotPlot	Plot dot plot showing expression of a gene set across cell types.
plotHeatmap	Plots symmetric AUROC heatmap, clustering cell types by similarity.
plotHeatmapPretrained	Plots rectangular AUROC heatmap, clustering train cell types (columns) by similarity, and ordering test cell types (rows) according to similarity to train cell types..
plotMetaClusters	Plot meta-cluster badges, each badge is a small AUROC heatmap restricted to a specific meta-cluster.
plotUpset	Plot Upset plot showing how replicability depends on input dataset.
scoreMetaClusters	Summarize meta-cluster information in a table.
splitClusters	Split clusters according to symmetric AUROC similarity.
splitTestClusters	Split test clusters according to AUROC similarity to train clusters.
splitTrainClusters	Split train clusters according to AUROC similarity to test clusters.
standardizeLabel	Remove special characters ("|") from labels to avoid later conflicts
subsetClusterGraph	Subset cluster graph to clusters of interest.
topHits	Find reciprocal top hits
topHitsByStudy	Find reciprocal top hits, stratifying results by study.
trainModel	Pretrains model for the unsupervised version of MetaNeighbor
variableGenes	Identify a highly variable gene set