Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

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Documentation for package ‘CelliD’ version 1.8.1

• 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