# Single cell replicability analysis

## Documentation for package ‘MetaNeighbor’ version 1.12.0

- 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