hh1985 / peptagram

HTML5 interactive visualisations of proteomic experiments

PEPTAGRAM

peptagram generates a single-page HTML5 web-app to visualize proteomics analyses for:

1. a sequence overview of a single proteomics experiment (example),
2. a graphical comparison between multiple proteomics experiment (example).

The resulting HTML5 web-app is:

• instantly available: runs on any modern webbrowser
• cross-platform: everyone has a webbrowser
• self-contained: just zip directory and send by email
• publishable: installable on any server, even on Dropbox

More information at http://boscoh.github.io/peptagram.

Installation

peptagram consists of a set of python scripts that converts proteomics data into an HTML5 visualisation.

To generate the visualisations, you must have python installed. If you have the python installer pip, then:

> pip install peptagram

Otherwise, download and unzip the package from https://github.com/boscoh/peptagram/archive/master.zip

And install from the package directory:

> python setup.py install

peptagram has two python dependencies:

1. pymzml to read .mzML files
2. uniprot to get protein sequences from http://uniprot.org.

These should be installed automatically from the above scripts, but if that fails, you may need to install them manually.

Usage

1. User guide to the HTML5 visualisation http://boscoh.github.io/peptagram/vizhelp.html.

2. Examples for generating visualisations from standard formats http://boscoh.github.io/peptagram/vizgen.html.

3. Programming API to use custom data http://boscoh.github.io/peptagram/api.html.

4. Source code and open-source contributions http://github.com/boscoh/peptagram.

Credits

Contributors: Rob Goode.
Original concept by Oded Kleifeld.
Developed at the Monash Proteomics Facility.
Copyright (c) 2013, Bosco K. Ho.

Changelog

0.2.1

• separated the delete_empty_proteins out in the proteins module