mdjones / proteomics-scripts

Fork of NomuraRG -- General scripts for proteomics data processing

README

What is this repository for?

This is a fork of proteomics-scripts (https://github.com/NomuraRG/proteomics-scripts). Whis is described as "General scripts for proteomics data processing"

We are working to harmonize processing of IP2 data (http://manual.integratedproteomics.com/#/) and Proteome Discover (https://www.thermofisher.com/order/catalog/product/OPTON-30795) data.

How do I get set up?

Dependencies

Package and enviornment managment is done with conda. Miniconda is sufficient. If you want to use the notebooks use Conda. You can also install conda after Miniconda is installed.

$ conda install anaconda

https://conda.io/docs/user-guide/install/index.html#regular-installation

Install and test

To install create the environment do the following.

$ git clone https://github.com/mdjones/proteomics-scripts.git
$ cd proteomics-scripts
$ REQS=" nose sqlalchemy pandas matplotlib seaborn scipy pip jupyter"
$ conda create -c conda-forge --prefix ./conda_env ${REQS}
$ pip install http://nrusca-ldl30114.nibr.novartis.net/~jonesmic/projects/2018/pd_reader/dpro-0.1.0rc1_snapshot-py3-none-any.whl
$ source activate nb-cpact
$ nosetests -s

Note: Look into pyproteome

Contribution guidelines

• Writing tests
• Code review
• Other guidelines

Who do I talk to?

proteomics-scripts

General scripts for proteomics data processing