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| CelliD-package | Multiple Correspondence Analysis on Single Cell for Joint Dimensionality Reduction of Gene and Cell, Cells Geneset Extraction and Geneset Enrichment Analysis |
| CelliD | Multiple Correspondence Analysis on Single Cell for Joint Dimensionality Reduction of Gene and Cell, Cells Geneset Extraction and Geneset Enrichment Analysis |
| checkCelliDArg | Check for CelliD arguments |
| checkCelliDArg.Seurat | Check for CelliD arguments |
| checkCelliDArg.SingleCellExperiment | 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 |
| GetCellGeneDistance.Seurat | Distance Calculation |
| GetCellGeneDistance.SingleCellExperiment | Distance Calculation |
| GetCellGeneRanking | Ranking Extraction |
| GetCellGeneRanking.Seurat | Ranking Extraction |
| GetCellGeneRanking.SingleCellExperiment | Ranking Extraction |
| GetCellGeneSet | Gene sets extraction from MCA |
| GetCellGeneSet.Seurat | Gene sets extraction from MCA |
| GetCellGeneSet.SingleCellExperiment | Gene sets extraction from MCA |
| GetGeneCellCoordinates | GeneCellCoordinates |
| GetGroupCoordinates | Centroids Coordinates |
| GetGroupCoordinates.matrix | Centroids Coordinates |
| GetGroupCoordinates.Seurat | Centroids Coordinates |
| GetGroupCoordinates.SingleCellExperiment | Centroids Coordinates |
| GetGroupGeneDistance | Centroids-Genes distances |
| GetGroupGeneDistance.Seurat | Centroids-Genes distances |
| GetGroupGeneDistance.SingleCellExperiment | Centroids-Genes distances |
| GetGroupGeneRanking | Gene Specificity Ranking Calculation |
| GetGroupGeneRanking.Seurat | Gene Specificity Ranking Calculation |
| GetGroupGeneRanking.SingleCellExperiment | Gene Specificity Ranking Calculation |
| GetGroupGeneSet | Extract cluster/group gene sets from MCA |
| GetGroupGeneSet.Seurat | Extract cluster/group gene sets from MCA |
| GetGroupGeneSet.SingleCellExperiment | 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 |
| RunCellGSEA.Seurat | Run Gene Set Enrichment Analysis on cells |
| RunCellGSEA.SingleCellExperiment | Run Gene Set Enrichment Analysis on cells |
| RunCellHGT | Run HyperGeometric Test on cells |
| RunCellHGT.Seurat | Run HyperGeometric Test on cells |
| RunCellHGT.SingleCellExperiment | Run HyperGeometric Test on cells |
| RunGroupGSEA | Run GSEA on cluster/groups |
| RunGroupGSEA.Seurat | Run GSEA on cluster/groups |
| RunGroupGSEA.SingleCellExperiment | Run GSEA on cluster/groups |
| RunMCA | Run Multiple Correspondence Analysis |
| RunMCA.matrix | Run Multiple Correspondence Analysis |
| RunMCA.Seurat | Run Multiple Correspondence Analysis |
| RunMCA.SingleCellExperiment | Run Multiple Correspondence Analysis |
| RunMCDMAP | Diffusion Map on MCA coordinates |
| RunMCDMAP.Seurat | Diffusion Map on MCA coordinates |
| RunMCDMAP.SingleCellExperiment | Diffusion Map on MCA coordinates |
| RunMCTSNE | tSNE on MCA coordinates |
| RunMCTSNE.Seurat | tSNE on MCA coordinates |
| RunMCTSNE.SingleCellExperiment | tSNE on MCA coordinates |
| RunMCUMAP | UMAP on MCA coordinates |
| RunMCUMAP.Seurat | UMAP on MCA coordinates |
| RunMCUMAP.SingleCellExperiment | UMAP on MCA coordinates |
| setDimMCSlot | SetDimSlot |
| setDimMCSlot.Seurat | SetDimSlot |
| setDimMCSlot.SingleCellExperiment | SetDimSlot |
| seuratPbmc | Seurat object of 400 PBMC cells |