Update GSVA to new API #774
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Hm, should we track down this diagram too? Everything else looks good!
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sjspielman
approved these changes
Jun 17, 2024
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Closes #770
Serendipitously closes #354
The GSVA interface changed in Bioc 3.18, so I am updating to the new API here. I added a couple sentences about the interface immediately before the chunk in question, but that other than that there should not be much that is surprising here.
Adding parallelism got a bunch easier too, or I had more experience since filing #354, so I happened to close that along the way.
Updated the rendering script to not skip the pathway analysis, so hopefully this will catch anything else that might be lingering as well!
I do think we will want to give these notebooks a once-over before we use them again, but this at least gets them working.