search

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
Other
100 stars 67 forks source link

Updated analysis? update a few cancer group abbreviations #1306

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

What analysis module should be updated and why?

Script here, plus figure 1B panel https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/figures/palettes/broad_histology_cancer_group_palette.tsv

What changes need to be made? Please provide enough detail for another participant to make the update.

To be consistent with subtyping module output, we should update: Ganglioglioma from GG --> GNG Ependymoma can be abbreviated EPN Craniopharyngioma from CP --> CRANIO

I wasn't sure where the abbreviation code for this palette is..

What input data should be used? Which data were used in the version being updated?

histology file

When do you expect the revised analysis will be completed?

this week

Who will complete the updated analysis?

@sjspielman @jaclyn-taroni or @jharenza

sjspielman commented 2 years ago

I added these abbreviations specifically to get the Figure 1 sample distribution in a manageable size. They are encoded in figures/mapping-histology-labels.Rmd. I can update these.