Cell type annotation tool for single cell data
Author and Maintainer: Hua Sun
Version: v0.3.1
The CTE4SO is a cell type annotation tool developed based on ScType (Ianevski et al., Nat Commun 2022). It was built for 10xMultiome project and specifically solve brain tissue annotation. Its characteristics are simplicity, convenience, ease of use and strong scalability. It is suitable for directly using Seurat4/5 objects for cell type annotation of scRNA/snRNA/snMultiome data. Currently contains a limited set of brain markers. It will continue to be upgraded as needed in the future.
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[ Notice ]
Most cell type markers were collected from normally developing brains, with a few marker sets coming from ependymomas (tumors). If a marker was collected from tumor data, it will be labeled "-Like" and annotated in the "Region" column as coming from that tumor type. This is because these marker sets were created for analysis of healthy brains and ependymoma brain tumors. (2024-10-04)
R >= 4.2.1
Seurat 4/5
dplyr
HGNChelper
readxl
dplyr
this.path
GetoptLong
ggplot2
--tissue 'Brain' # Tissue name. Default: 'Brain'
--db 'hs.brain' # Human brain cell type annotation
'mm.brain.v2' # Mouse brain cell type annotation
'sctype.beta' # Beta marker set for cell type annotation
...
--rds '' # Seurat object file (.rds)
--assay 'SCT' # Seurat assay type. SCT(Default)/RNA/...
--plot # Plot UMAP
--title '' # Title in plot. Default:''
--reduction 'umap' # Reduction in plot. Default:'umap'
--groupby 'cell_type2' # Group by in plot. Default:'seurat_clusters,cell_type,cell_type2'
--save # save annotated rds
--outdir out_celltype (default) # output directory
- Test
Rscript cte4so.R --rds scrna.rds --db hs.brain --assay SCT --outdir out_celltype
output: cluster_cellType.xls, metaData.cellType.xls
Rscript cte4so.R --rds scrna.rds --db hs.brain --assay SCT --outdir out_celltype --plot
output: cluster_cellType.xls, metaData.cellType.xls, ...umap.pdf
- Save cell type to seurat object
Rscript cte4so.R --rds scrna.rds --db hs.brain --assay SCT --outdir out_celltype --save
output: cluster_cellType.xls, metaData.cellType.xls, sc_celltype_anno.rds
If you use this tool or the cell type marker set in your research/analysis, please cite github.com/combiozone/CellTypeEstimate
Hua Sun, hua.sun@stjude.org ; Stephen Mack (PI) stephen.mack@stjude.org