# Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

## Documentation for package ‘CelliD’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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