GenePattern R package?

[Sara Haddock]

Hi GenePattern team,

I'm trying to run GenePattern modules within R.  According to the instructions here, I should be able to find the R package in "Downloads>Programming Libraries" within GenePattern.  I don't see that anywhere.  Can anyone help?

Thanks so much,

-Sara

[Thorin Tabor]

Hello Sara,

The old GenePattern R package was deprecated and removed because it no longer works with recent versions of R.

That said, you should still be able to access GenePattern modules and launch GenePattern jobs using the GenePattern REST API. Unfortunately it's a bit more work, but from R you can load the httr and jsonlite packages, then call the endpoints described in the GenePattern REST API documentation.

https://www.genepattern.org/rest-api

If you're familiar with Python, we also have a Python library that is available.

https://github.com/genepattern/genepattern-python

Thorin Tabor
GenePattern Team

--
You received this message because you are subscribed to the Google Groups "GenePattern Help Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genepattern-he...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/42be8bd8-3eea-4018-8c50-b27871fe0c3fn%40googlegroups.com.

[Sara Haddock]

ok, that makes sense.  Can the Programmers' Guide be edited to reflect that?  I'm not the only one who's been confused by this.

Thanks so much for your help, and happy holidays.

-Sara