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Question: Analysis of Galaxy Cuffdiff output by CummeRbund
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gravatar for paadd
3.1 years ago by
paadd • 0
United Kingdom
paadd • 0 wrote:

Hi,

I am trying to use cummeRbund in Rstudio to analyse my Galaxy Cuffdiff output. However I am having trouble creating a database. Should I be using the tabular files generated by Cuffdiff or the SQlite database option. Are both of these outputs currently compatible with cummeRbund in R studio? Thanks for any help.

Andrew
cummerbund cufflinks • 1.7k views
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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by paadd • 0
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gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Cuffdiff inputs are compatible with cummeRbund as wrapped for Galaxy. I am not personally familiar enough with the tech requirements of Rstudio to comment on the compatibility with the stand-alone version with a definitive answer (but someone else reading may be).

We plan to test this specifically (Galaxy Cdiff output with stand-alone Rstudio, would be good to know), but don't wait for us. Going forward with your own testing is the quickest path to work out usage for 3rd party apps not integrated into Galaxy. Perhaps just try the SQlite to see if that works?

I can let you know that Galaxy-Rstudio integration has some development in progress, but it is not ready for use by most. Implementation is "non trivial" according to the developers working on this and would be best on a local if you want to give it a go. 

"These instructions should cover setting up RStudio and IPython for 15.07 or later https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/interactive_environments.rst" via jmchilton

Hopefully this helps you to move forward! Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
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