Mapping and Analysis of Phosphorylation Pathways Identified through Network/Graph Signalling
Project 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)
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