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.
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
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
- Writing tests
- Code review
- Other guidelines
General scripts for proteomics data processing