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What is BD-Func?

BD-Func (Warden et al. 2013) is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns.

How can I cite COHCAP?

Charles D. Warden, Noriko Kanaya, Shiuan Chen, and Yate-Ching Yuan (2013) BD-Func: A Streamlined Algorithm for Analysis of Activation and Inhibition of Pathways peerJ 1:e159.

Other FAQs

[What is the format for the parameter file?]
[What is the format for the signal file?]
[What is the format for the enrichment file?]
[What sort of figure can I expect from BD-Func?]
[Why can't I run BD-Func GUI?]
[How do I know that Java JDK is installed correctly?]
[How do I know that Perl is installed correctly?]
[I have pointed R to Rscript.exe in Windows - why doesn't BD-Func run properly?]
[Why do I get an error message saying there is no package called 'qvalue'?]
[Why do I get an error message saying there is no package called 'ROCR'?"]
[Why do I get an error message saying that Windows can't spawn cmd.exe"]

Common Problems & Solutions

Problem: BD-Func cannot open a file
Possible Solution: Make sure that no files, folders in path to files, or groups have spaces. This will cause the program to crash.

I still need help!

If the BD-Func user manual, FAQ links above, or discussion board cannot help you with your problem, you may contact Charles Warden (cwarden [at] coh [dot] org]) for trouble-shooting support. However, we strongly encourage users to post their problems on the message board because they may be helpful to other users.