Man pages for Cortalak/cellID
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
| cellID-package | Multiple Correspondence Analysis on Single Cell for Joint... |
| checkCellIDArg | Check for CellID arguments |
| DimPlotMC | Seurat DimPlot for MCA like Dimensionality Reduction |
| DistSort | Sort Gene Cell Distance Matrix |
| fgseaCellID | reworked fgsea for ram and speed efficiency in CellID |
| GetCellGeneDistance | Distance Calculation |
| GetCellGeneRanking | Ranking Extraction |
| GetCellGeneSet | Gene sets extraction from MCA |
| GetGeneCellCoordinates | Get coordinates of both cells and features in a matrix |
| GetGroupCoordinates | Centroids calculation for a given group |
| GetGroupGeneDistance | Distance calculation between genes and group |
| GetGroupGeneRanking | Gene Specificity Ranking Calculation |
| GetGroupGeneSet | Extract cluster/group gene sets from MCA |
| GetGSEAMatrix | Get Matrix from Enrichment Results |
| GO_biological | Biological Process GO Terms |
| Hallmark | Hallmark Pathways from MSigDB |
| HgProteinCodingGenes | Homo Sapiens Protein Coding Genes |
| import | Import |
| integrateGSEASeurat | GSEA Results Integration in Seurat object |
| MgProteinCodingGenes | Mus Musculus Protein Coding Genes |
| pairDist | Distance Calculation with rdist |
| plotReducedDimMC | Scater plotReducedDim for MCA like dimensionality Reduction |
| RunCellGSEA | Run Gene Set Enrichment Analysis on cells |
| RunCellHGT | Run HyperGeometric Test on cells |
| RunGroupGSEA | Run GSEA on cluster/groups |
| RunMCA | Run Multiple Correspondence Analysis |
| RunMCDMAP | Run DiffusionMap on MCA cell and feature coordinates |
| RunMCTSNE | Run TSNE on MCA fetures and cells coordinates |
| RunMCUMAP | Run UMAP on MCA fetures and cells coordinates |
| setDimMCSlot | SetDimSlot |
| seuratPbmc | Seurat object of 400 PBMC cells |
