Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq

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Documentation for package ‘scGOclust’ version 0.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

analyzeGOSeurat	standard seurat analysis on GO_seurat object
cellTypeGOCorr	calculate correlation between cell types represented by scaled GO, per-species
crossSpeciesCellTypeGOCorr	calculate cross-species correlation between cell types represented by scaled GO
dme_subset	Drosophila gut scRNA-seq data, 10X Chromium Subset to 45 cells per cell type as an example data
dme_tbl	Drosophila EMSEMBL gene and GO annotation, subset to genes present in 'dme_subset'
ensemblToGo	get requested ensembl ID to GO mapping table
getCellTypeGO	get per cell type average scaled vector of GO terms
getCellTypeSharedGO	get shared up and down regulated GO terms for all pairs of cell types
getCellTypeSharedTerms	query co-up and co-down regulated GO terms from certain cell type pairs
globalvariables	record some global variables: pre-defined column name in biomaRt query and markers
makeGOSeurat	create a seurat object with GO terms
mmu_subset	Mouse stomach and intestine scRNA-seq data, microwell-seq Subset to 50 cells per cell type as an example data
mmu_tbl	Mouse EMSEMBL gene and GO annotation, subset to genes present in 'mmu_subset'
plotCellTypeCorrHeatmap	plot clustered heatmap for cell type corr
plotCellTypeSankey	plot Sankey diagram for cell type links above a certain threshould