Man pages for RausellLab/CelliD
Unbiased Extraction of Single Cell gene signatures 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 | Slight change in fgsea for ram and speed efficiency in CelliD |
| GetCellGeneDistance | Distance Calculation |
| GetCellGeneRanking | Ranking Extraction |
| GetCellGeneSet | Gene sets extraction from MCA |
| GetGeneCellCoordinates | GeneCellCoordinates |
| GetGroupCoordinates | Centroids Coordinates |
| GetGroupGeneDistance | Centroids-Genes distances |
| GetGroupGeneRanking | Gene Specificity Ranking Calculation |
| GetGroupGeneSet | Extract cluster/group gene sets from MCA |
| GetGSEAMatrix | Get Matrix from Enrichment Results |
| Hallmark | Hallmark Pathways from MSigDB |
| HgProteinCodingGenes | Homo Sapiens Protein Coding Genes |
| import | Import |
| MgProteinCodingGenes | Mus Musculus Protein Coding Genes |
| pairDist | Distance Calculation |
| 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 | Diffusion Map on MCA coordinates |
| RunMCTSNE | tSNE on MCA coordinates |
| RunMCUMAP | UMAP on MCA coordinates |
| setDimMCSlot | SetDimSlot |
| seuratPbmc | Seurat object of 400 PBMC cells |
