PeltzLab-Stanford / mMap

Computational tool for prioritizing the genetic candidates based on the protein functional and regulatory features

Introduction

Python implementation of Mouse Genome Genotype to Phenotype mapping method for the prioritizing the genetic candidates based on the protein functional and genomic regulatory features

installation

pip install -i https://test.pypi.org/simple/ mgMap==0.0.2 --target=/path/where/to/install/ && cd mgmap

usage

python3 mgmap.py -g filename.txt (see Exmaple datafiles "gene.txt" for exact format)

python3 mmgap.py -nc filename.txt (see Exmaple datafiles "regulatory.txt" for exact format)

PS:

The Functional data folder contains a help file for more information

The Regulatory data folder contains a help file for more information

output

For details of output files, see Wiki

compatibility

The package is compatibility with both Windows and Mac setup.

requirements

python 3

R (see R folder for more information)

tree

The package can be used to analyse the impact of mutations on the protein functional regions like domains and PTM sites. Also, for regulatory regions like Promoter, enhancer etc.

  File tree
  ./mgmap/
     mgmap.py
     user's input data-file.txt
     /Functional datafiles/Functional-data.txt
     /Functional datafiles/conservation/
     /Functional datafiles/numbers/
     /Functional datafiles/Phenotype.txt
     /Regulatory datafiles/Vista_enhancers_flankinGenes.txt
     /Regulatory datafiles/EPDnew_promoter.txt
     /Regulatory datafiles/TSS_promoter.txt
     /Regulatory datafiles/cpgIsland.txt
     /Regulatory datafiles/insulator-CTCF-binding-sites.txt

contact

email: [e-mail]

visit: https://mmap.stanford.edu/