bioconda PyPI https://github.com/wfondrie/ppx/workflows/tests/badge.svg?branch=master Documentation Status

A Python interface to proteomics data repositories

ppx provides simple, programmatic access means to access proteomics data that are publicly available in ProteomeXchange 1 partner repositories. ppx allows users to easily find and download files associated with projects in PRIDE 2 and MassIVE 3.

Our intent is that ppx would provide an efficient method to reuse proteomics data that has been deposited in public repositories, thereby promoting reproducible research practices and enabling tool developers.

Installation

ppx requires Python 3.6+ and depends upon the requests and tqdm Python packages. ppx and any missing dependencies can be installed with pip: or conda.

Install with conda:

conda install -c bioconda ppx

Or install with pip:

pip install ppx

License

ppx is distributed under the MIT license.

For R Users

ppx was inspired by the rpx R package 4 written by Laurent Gatto. If you are an R user and want many of the same functionalities that ppx offers, check it out on Bioconductor <http://bioconductor.org/packages/release/bioc/html/rpx.html> and GitHub.

1

Vizcaino J.A. et al. ProteomeXchange: globally co-ordinated proteomics data submission and dissemination, Nature Biotechnology 2014, 32, 223 – 226, doi:10.1038/nbt.2839.

2

Vizcaíno JA, et al. 2016 update of the PRIDE database and related tools. Nucleic Acids Res. 2016, 44(D1): D447-D456. doi:10.1093/nar/gkv1145.

3

Wang M, et al. Assembling the Community-Scale Discoverable Human Proteome. Cell Syst. 2018 Oct 24;7(4):412-421.e5. doi: 10.1016/j.cels.2018.08.004.

4

Gatto L. rpx: R Interface to the ProteomeXchange Repository. 2018, R package version 1.16.0, https://github.com/lgatto/rpx.