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Rerun recount2 notebooks #36

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merged 8 commits into from
Oct 13, 2020
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@ajlee21 ajlee21 commented Oct 10, 2020

This PR is rerunning the notebooks using all SRA data from recount2. No code was changed in this PR. This PR is re-running the notebooks to get the cell outputs that were previously cleared. This should address #25

Minor changes include:

  • Rename the analysis direction from human_analysis to human_general_analysis to make way for adding a new analysis where we're training only on cancer-specific gene expression data. As opposed to recount2, which contains general gene expression data.

Note:

  • I tried to train the model on 20 epochs as opposed to 40, since 20 seems sufficient based on the log plot. When I was running the notebook the internet connection crashed so the model training progress was lost. I have made an issue here. Since models were already trained and uploaded in this PR, I used these files to run the analysis notebook.

@ajlee21 ajlee21 requested a review from dongbohu October 13, 2020 01:16
@ajlee21 ajlee21 marked this pull request as ready for review October 13, 2020 01:16
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Looks good!

@ajlee21 ajlee21 merged commit 3489cc1 into greenelab:master Oct 13, 2020
@ajlee21 ajlee21 deleted the recount2_rerun branch October 13, 2020 21:54
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