working with mgMap
Move file to the mgmap folder and run the following command for input file contains genomics coordinates of mutations
- python3 mgmap.py -nc inputfile
For input file, with protein level residue alterations, run the following command:
- python3 mgmap.py -g inputfile
Expected output should contain the following files:
- file with (i) proteins or gene names (depending on the input file) with (ii) mutations of interest, (iii) functional or regulatory regions where these mutations can be mapped, (iv) conservation of each mutated residue position see here.
- graph showing the number of mutations per gene/protein and conservation of each mutated positions
- files containing the output for the following analyses:
GO term enrichment test 
biological pathways enrichment test (
biological processes enrichment test example 
significantly mutated protein functional or genome regulatory regions example 
protein network analysis 
single cell expression data of proteins/genes with mutations "example ":https://github.com/PeltzLab-Stanford/mMap/blob/master/Example%20results/ExampleResults_scExpression-data.txt
- All the files (text and png) are saved in the output folder with the same name as input file.
- For the better seamless view, we also generate an elegant html page contains all the visualizations.