Metadata-Version: 2.1
Name: margo
Version: 0.0.4
Summary: A tool that generates yaml cell type marker which maps cell types to gene expression.
Home-page: https://github.com/camlab-bioml/margo
Author: Jinyu Hou
Author-email: jhou@lunenfeld.ca
License: GPLv2
Description: .. margo documentation master file, created by
           sphinx-quickstart on Wed Aug  5 09:18:37 2020.
           You can adapt this file completely to your liking, but it should at least
           contain the root `toctree` directive.
        
        **************************
        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 <https://camlab-bioml.github.io/margo/>`_.
        
        --------------
        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 |text|_ (Website: http://biocc.hrbmu.edu.cn/CellMarker).
        
        .. _text: https://academic.oup.com/nar/article/47/D1/D721/5115823
        
        .. |text| replace:: *CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Research. 2018.*
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
