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

## 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