Margo (Marker Generator)

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).