GOhuman                 GOhuman
GOmouse                 GOmouse
MetaNeighbor            Runs MetaNeighbor
MetaNeighborUS          Runs unsupervised version of MetaNeighbor
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.
makeClusterGraph        Convert AUROC matrix into a graph.
makeClusterName         Make cluster names in format
                        'study_id|cell_type'
mergeSCE                Merge multiple SingleCellExperiment objects.
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
