Galaxy: how you can do genomic analyses (when you are not a programmer)

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ryan_m
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Galaxy: how you can do genomic analyses (when you are not a programmer)

I suggest that anyone conducting some genome-scale analysis should start with Galaxy. The creators describe it as a "web-based data analysis framework that allows you to collect and work with biological data from many different sources". I have been using it for some time, mainly for one-off analyses or to prototype something I plan to implement in a pipeline (to see whether it is worthwhile). It interacts with UCSC genome browser as well as the EnsEMBL ENSMART/BioMart system to get data, though you can also upload your own data if you want. Try it, and It would be good to have some user feedback posted here as well.

Ryan

bgood
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I haven't had time to play

I haven't had time to play with this thing yet, but it seems worthwhile.

Can you get expression information associated with particular genomic regions (ESTs, GEO??)

If yes, how is the context of the expression indicated / queried ?

ryan_m
ryan_m's picture
Good question. I haven't

Good question. I haven't tried to use it for anything related to gene expression. They have a good wiki describing what tools are currently available (see original post). They also have been very fast to respond to my questions in the past.

Ryan