MQ Summer School tutorial for Perseus plugin development. The plugin development tutorial consists of two parts. Make sure to have all the requirements installed.
Most functionality in Perseus is implemented in C#, by following the plugin API (see online). We will develop our own simple plugin by modifying the most simple existing plugin (clone matrix). In the end the plugin will allow us to extract a number of rows from the top of the matrix as specified by a parameter.
Navigate to the /PluginTutorial folder for more information.
See in PluginTutorial README.
Besides the plugin in this repository you can check out:
- PluginUpperCase is a simple plugin to change all strings to upper case.
Recently we have started to develop a light-weight approach to plugin programming. We aim to enable you to use popular scripting languages such as R and Python from within Perseus. We will see, how to implement the same functionality as before in R and Python instead of C#.
Navigate to the /scripts folder for more information.
See in scripts README.
We recommend installing the Anaconda Python distribution
(Python 3.X 64bit). In the installer make sure to enable the option to add Python to your
PATH.
Next you should install the perseuspy module.
If python is in your PATH you should be able to open a Command Prompt (search for cmd.exe) and
type in the installation instructions from the perseuspy website.
First install the latest version of R. We recommend to additionally install R Studio Desktop.
Next install the PerseusR package. Open R Studio and enter the instructions on the website into the running R session.
Besides the plugin scripts in this repository you can check out:
- PluginDependentPeptides is a plugin for reading the dependent peptide search results into Perseus. This plugin is a hybrid of C# code for parameter passing and a Python script for the actual processing.