Metadata-Version: 1.1
Name: mappings
Version: 0.0.1
Summary: Mapping and Analysis of Phosphorylation Pathways Identified through Network/Graph Signalling
Home-page: https://github.com/finnod/mappings
Author: Finn O'Donoghue
Author-email: finnodonoghue@gmail.com
License: UNKNOWN
Description: # 🗺 MAPPINGS v0.0.1
        
        ## Mapping and Analysis of Phosphorylation Pathways Identified through Network/Graph Signalling
        
        Mappings is a tool for blah blah. 
        
        It analyses kinexus chip data to find..
        
        Maybe put a picture here or something. The sky is the limit.
        
        First described by our names here: (Not the real article, but just showing you can put links)
        
        [Network analysis of large phospho-signalling datasets: application to Plasmodium-erythrocyte interactions](https://www.biorxiv.org/content/10.1101/2021.05.07.443051v1)
        
        and it looked pretty good doing it!
        
        ![Alt text: complex network structures](https://www.biorxiv.org/content/biorxiv/early/2021/05/07/2021.05.07.443051/F2.large.jpg?width=800&height=600&carousel=1)
        
        Designed and programmed with love by Dr. Jack Adderley and Finn O'Donoghue.
        
        ## Installation
        
        	pip install mappings
        
        ## Usage
        
        	mappings [OPTIONS] ARRAY_DATA_PATH OUTPUT_PATH
        
        or 
        
        	python -m mappings [OPTIONS] ARRAY_DATA_PATH OUTPUT_PATH
        
        ### Options
        
        	  --nwalks INTEGER                Number of walks.
        	  --connection_network_path PATH  Network of known phosphorylation connections.
        
        
        ## Input / Output Specification
        
        ### Array Data
        Sort of comes from kinexus.
        
        CSV file with headers:
         - Uniprot ID
         - Protein
         - Phospho Site (Human),
         - UMean
         - UMean Error (%)
         - TMean
         - TMean Error (%)
        
        ### Output Data
        For use in Cytoscape or some other analysis program.
        
        CSV file with headers:
        
        - Kinase
        - Substrate
        - cdf_x
        - INVLog2FoldChange 
        - ...etc
        
        ### Connection  Network
        Accumulated from literature reports. Updated version may be available under `data/input/NetworkComplete.csv`
        Please email the authors, or submit a pull request to update this file with any new data.
        
        CSV file with headers:
        - Phosphosite
        - Kinase_uniprot_ID
        - Substrate_uniprot_ID
        - SubID_phosphosite
        - Substrate_effect
        - Kinase
        - Substrate
        
        ## Publications
         - ...et al. 2021
         - [Review by highly respected bioinformatics group et al., 2022](https://www.google.com/search?q=most+important+bioinformatics+tools+of+all+time)
Keywords: mapping,analysis,phosphorylation,pathways,network,graph,signalling,kinase,kinases,kinexus,protein,informatics,bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Intended Audience :: End Users/Desktop
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
