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cognoma / cancer-data

TCGA data acquisition and processing for Project Cognoma
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Update Data for April 2018 TCGA PanCanAtlas Data Release #41

Closed gwaybio closed 6 years ago

gwaybio commented 6 years ago

closes #40

Updating 0, 1, and 2 numbered scripts in this repo to:

  1. update cognoma genes to draw from cognoma/genes#4 (script 0).
  2. download updated PanCanAtlas Data from UCSC Xena (script 1). This includes updated mutation, gene expression, and clinical data.
  3. process updated PanCanAtlas data (script 2)

As a result, all output data are also updated. We should update the figshare once this is merged accordingly.

dhimmel commented 6 years ago

As a result, all output data are also updated. We should update the figshare once this is merged accordingly.

Yes, although if you had plans to use this immediately, you may want to use it from commit hash for a few days, in case any issues arise. I didn't review every dataset carefully. But I'm also fine with updating the fighsare immediately. @gwaygenomics do you think you'll have additional changes / fixes in the next few days?

gwaybio commented 6 years ago

Yes, although if you had plans to use this immediately, you may want to use it from commit hash for a few days, in case any issues arise. I didn't review every dataset carefully. But I'm also fine with updating the fighsare immediately. @gwaygenomics do you think you'll have additional changes / fixes in the next few days?

I probably wasn't going to use immediately - still more prototyping to do with other things - but I am aiming to use this data by the end of the third week in April. I think it would be great to double check these datasets, but I wanted to get the ball rolling on it! (I probably won't have any updates the next few days).

I will go ahead and squash merge now, but I think that updating the figshare after another review is a good idea