Man pages for PolinaPavlovich/CONCLUS
ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.
| addClusteringManually | addClusteringManually |
| calculateClustersSimilarity | Having cells similarity, calculate clusters similarity. |
| choosePalette | Choose palette for a plot. |
| clusterCellsInternal | Cluster cells and get similarity matrix of cells. |
| exportClusteringResults | exportClusteringResults |
| exportMatrix | Export matrix to a file. |
| generateTSNECoordinates | Generate and save t-SNE coordinates with selected parameters. |
| getGenesInfo | Collect genes information to one table. |
| getMarkerGenes | Get top N marker genes from each cluster. |
| initialisePath | Create all needed directories for CONCLUS output. |
| normaliseCountMatrix | normaliseCountMatrix |
| plotCellHeatmap | Save markers heatmap. |
| plotCellSimilarity | Save a cells similarity matrix. |
| plotClusteredTSNE | Plot t-SNE. Addtionally, it can highlight clusters or states. |
| plotClustersSimilarity | Save a similarity cluster matrix. |
| plotGeneExpression | plotGeneExpression |
| rankGenes | Rank marker genes by statistical significance. |
| runClustering | DBSCAN clustering on t-SNE results. |
| runCONCLUS | Run CONCLUS in one click |
| runDBSCAN | Run clustering iterations with selected parameters using... |
| saveGenesInfo | Save gene information into a table or tables for multiple... |
| saveMarkersLists | Save top N marker genes for each cluster into a format... |
| testClustering | To check one iteration of clustering before running full... |
