Add MMRF-COMMPASS cohort

[maryjgoldman]

Let Keith know when it's out.

[felixfrenkel]

Hi, Mary!

I am looking for MMRF COMPASS kallisto expression profiles.
Are you going to generate them?

Regards, Felix

[maryjgoldman]

Hi Felix!

The Toil group at UCSC generated Kallisto outputs on TCGA, TARGET, and GTEx. You can ask them to run more samples through their pipeline though I am not sure their funding for this (reach out to them via their website here: https://toil.ucsc-cgl.org/). That said, the pipeline is available for anyone to run. If you or someone you know has run the MMRF COMMPASS samples through the Toil pipeline, let us know.

Also, please feel free to reach out again but I am going to close this issue since the MMRF COMMPASS cohort with the GDC-provided expression is now available here: https://xenabrowser.net/datapages/?cohort=GDC%20MMRF-COMMPASS. Forgot to close this issue when it went out!

Best,
Mary

[ayan-b]

Hi Mary,

The MMRF-COMMPASS script is not in the master branch. It is here #97. Just wanted to point out this so that it may save some time in the future! :)

[maryjgoldman]

Hi Ayan! Oh, good to know! We pushed out the initial data you generated but didn't merge the code. Re-opening this and will flag it for merging after the holidays. Thank you Ayan! Hope all is well with you.