Rokita/update survival

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR updates the survival analysis for CLK1 status:

• for HGGs, to use only those differentially spliced across all HGGs (>2 SD lower than mean) as low and the top 12 as high.
• for other cancers, to use those DS (>2 SD lower than mean) as the low clk1 exon 4 samples and those >1 SD from mean (>2 would be >1) as high.

I also removed NF1 scripts/code/outputs

What was your approach?

What GitHub issue does your pull request address?

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.

Documentation Checklist

• This analysis module has a README and it is up to date.
• The analytical code is documented and contains comments.

[jharenza]

@naqvia i think we can get this merged

[jharenza]

@naqvia can you review pls

[naqvia]

Looks good to me. Scripts run as expected