Version 21 (modified by b.hoekman@…, 9 years ago) (diff)



Galaxy servers as the main Graphical User Interface and framework for using the msCompare program in an easy and intuitive manner. To install msCompare in galaxy pls download (msCompare_For_Galaxy.tar.gz under downloads) and follow the installation details in the README file.

User Manual

General Data Processing Workflow in Galaxy

Galaxy Modules

Unfortunately not all modules are included at this moment in this list. However most other modules work similar to those explained in detail here.

LC-MS Data related

Settings Related

Feature Quantification

Feature Alignment & Matching

Feature Matrix Related

Example Server

NBIC is generously providing an "testing" server at which msCompare is hosted.
However at this location not all features of msCompare are installed.
The testing server can be found at:

A small dataset available for testing with galaxy can be found at:
The same dataset was processed (including statistics) the results can be found at:


  1. Working since (24-10-2010)
  2. Small bug in MZmine feature matrix when run with a fileSet (fixed 10-01-2010)

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