Man pages for MetaNeighbor
Single cell replicability analysis
| extendClusterSet | Extend cluster set to nearest neighbors on cluster graph. |
| extractMetaClusters | Extracts groups of reciprocal top hits from a 1-vs-best AUROC... |
| 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' |
| 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. |
| plotBPlot | Plot Bean Plot, showing how replicability of cell types... |
| plotClusterGraph | Plot cluster graph generated with makeClusterGraph. |
| plotDotPlot | Plot dot plot showing expression of a gene set across cell... |
| plotHeatmap | Plots symmetric AUROC heatmap, clustering cell types by... |
| plotHeatmapPretrained | Plots rectangular AUROC heatmap, clustering train cell types... |
| plotMetaClusters | Plot meta-cluster badges, each badge is a small AUROC heatmap... |
| plotUpset | Plot Upset plot showing how replicability depends on input... |
| 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... |
| splitTrainClusters | Split train clusters according to AUROC similarity to test... |
| standardizeLabel | Remove special characters ("|") from labels to avoid later... |
| subsetClusterGraph | Subset cluster graph to clusters of interest. |
| topHits | Find reciprocal top hits |
| trainModel | Pretrains model for the unsupervised version of MetaNeighbor |
| variableGenes | Identify a highly variable gene set |
