A tool that generates yaml cell type marker which maps cell types to gene expression.
Project description
Margo is a tool that generates yaml cell type marker which maps cell types to gene expression from csv gene expression files.
Checkout a full documentation here.
Installation
pip install margo
Usage
margo <input_csv> <output_yaml> -t/--tissue <specified_tissues> -m/--min_marker_per_celltype <min_marker_per_celltype>
The input file <input_csv> should be a csv file which contains single cell gene expression data. It must includes the feature names (gene markers) as the column names in the first row.
The output yaml file <output_yaml> is a marker which maps cell types to gene markers.
Here’s an example:
cell_type: Angiogenic T cell: - CD3 - CD31 Basal epithelial cell: - Vimentin - Cytokeratin 14 - Cytokeratin 5 CD1C-CD141- dendritic cell: - CD45 - CD68 Cancer cell: - CD44 - Cytokeratin 8/18 - Her2 - CD45 - CD20 Cancer stem cell: - CD44 - c-Myc Epithelial cell: - Cytokeratin 19 - Cytokeratin 8/18 - SMA Hematopoietic stem cell: - CD44 - CD45 Leukocyte: - CD3 - CD45 - CD20 Luminal epithelial cell: - Cytokeratin 19 - Cytokeratin 8/18 Myoepithelial cell: - CD44 - SMA - Cytokeratin 14
Reference
Marker data was extracted from database CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Research. 2018. (Website: http://biocc.hrbmu.edu.cn/CellMarker).
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