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d3b-center / pbta-splicing

Splicing analysis across the PBTA
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using oncokb #399

Closed naqvia closed 4 months ago

naqvia commented 4 months ago

Added oncoKB as geneList to determine TS/oncogenes. Related to issue #398

naqvia commented 4 months ago

Note: I removed other gene familys so that we could see the patterns better and focus on TSG/oncogenes only.

naqvia commented 4 months ago

Im okay with this! Lets do it like this; it is more clearer/cleaner.

jharenza commented 4 months ago

Im okay with this! Lets do it like this; it is more clearer/cleaner.

ok let me update dims and then will approve!

jharenza commented 4 months ago

hi @rjcorb would you mind reviewing this- we pulled in the new gene list from annofuse and only use tsg/oncogene in the plots now. I had to make some additional changes to downstream scripts, and reran the entire module.

jharenza commented 4 months ago

Looks good overall, but there are a few changed files that need to be added to this PR:

  • results/ctrl_vs_treated.de.formatted.tsv
  • results/ctrl_vs_treated.de.tsv

hmm re-running now

jharenza commented 4 months ago

Looks good overall, but there are a few changed files that need to be added to this PR:

  • results/ctrl_vs_treated.de.formatted.tsv
  • results/ctrl_vs_treated.de.tsv

per slack, these were output but not changed with a rerun..