update molecular subtyping methods

[rjcorb]

Purpose

Briefly describe your changes here.

This PR adds updated subtyping methods for the following tumor histologies:

• Craniopharyngioma
• Embryonal tumors (non-MB, non-ATRT)
• Ependymoma
• High-grade glioma
• Low-grade glioma
• Medulloblastoma
• Pineoblastoma

Issue

What GitHub issue does your pull request address?

#69 - #75

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

Which areas should receive a particularly close look?

Please review new text and ensure that this matches with respective histology subtyping flow diagrams in OpenPedCan-analysis module.

Is there anything that you want to discuss further?

Is the pull request ready for review?

Yes

Pull review checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

• All changes to text follow "one sentence per line" [Manubot instructions]
• All citations follow the Manubot citation instructions
• All changes or additions to tables follow the Manubot table instructions
• All figures follow the Manubot figure instructions
• There are no new spelling errors identified by the Manubot spellchecker

Spellcheck Step

The dictionary used for spellchecking can be updated.
Edit the file in build/assets/custom-dictionary.txt by adding new entries to the end.
You do not need to change anything else.
However, if you want to update the first line to have an accurate count of words and you want to remove non-unique ones, run the following command from within build/assets on your favorite OS X or Linux machine:

(( len = $(awk '!a[$0]++' < custom-dictionary.txt | wc -l ) - 1 )); tmpfile="$(mktemp)"; echo "personal_ws-1.1 en $len utf-8" > $tmpfile; tail -n +2 custom-dictionary.txt | awk '!a[$0]++' >> $tmpfile; mv $tmpfile custom-dictionary.txt

[github-actions]

Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit e745ecc.

Manuscript build

There were 73 spelling errors.
Check the build link above for details.

[jharenza]

few changes, but will approve pending those

[jharenza]

73

can you also check these spelling errors and update the dictionary with new words to add, alphabetize, and update wordcount at the top in https://github.com/d3b-center/OpenPedCan-methods/blob/main/build/assets/custom-dictionary.txt - thanks!

[github-actions]

Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit 905ba74.

Manuscript build

There were 70 spelling errors.
Check the build link above for details.

[github-actions]

Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit c909aa9.

Manuscript build

There were 70 spelling errors.
Check the build link above for details.

[github-actions]

Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit e673ffe.

Manuscript build

There were 0 spelling errors.
Check the build link above for details.