Re: questions about GO-Elite

[Nathan Salomonis]

Hi Pengcheng,

Actually both the compiled and source code versions of GO-Elite can run in fully headless modes (no GUI). The same is true for GO-Elite's parent application AltAnalyze which performs gene expression, QC, alternative splicing and many data visualization outputs (hierarchical clustering, network visualization, splicing plots, lineage correlations). GO-Elite is callable from AltAnalyze as well (command line and GUI).

http://code.google.com/p/go-elite/wiki/CommandLineMode

http://www.genmapp.org/go_elite/help.htm#commandline

http://code.google.com/p/go-elite/wiki/StandAloneDependencies

http://code.google.com/p/altanalyze/wiki/CommandLineMode

http://code.google.com/p/altanalyze/wiki/StandAloneDependencies

Best,

Nathan

On Jul 4, 2014, at 3:48 AM, Pengcheng Yang （杨鹏程） <yan...@mail.biols.ac.cn> wrote:

Dear Prof. Salomonis,

Thank you for your powerful and creative software GO-Elite. I like it for the following reason:
1. provide an another method to measure over representation, i.e. Z score and permutation based P-value.
2. Data structure for all OBO format file, so can do similar analysis for any Classification systems with OBO format file.
3. prune the resulted GO terms and give an non redundant GO set.

So, I want to integrate the GO-Elite into our analysis pipeline, especially for newly sequenced genome. As you have mentioned on the tutorial (http://www.genmapp.org/go_elite/help.htm#new_species), it can be done through the GUI interface. However, our pipeline most running at linux server without a GUI, and the analysis always done for a large number of gene sets, so it will be labor-intensively to use GUI. I wonder whether GO-Elite has a pure command line version that independent on Tkinter package.

Thank you!

Best,
Pengcheng Yang