| 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 |