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Update 03.methods.md #126

Merged
merged 6 commits into from
Sep 28, 2020
Merged

Update 03.methods.md #126

merged 6 commits into from
Sep 28, 2020

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jharenza
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@jharenza jharenza commented Sep 24, 2020

Purpose

Briefly describe your changes here.

  • Update CBTTC to CBTN
  • Add information about pathology_free_text_diagnosis
  • Clarify description integrated_diagnosis
  • Add cohort_participant_id to pbta-histologies.tsv metadata table
  • Update glioma_brain_region to CNS_region and update description
  • Update MB subtyping methods
  • Add url for PNOC

Issue

What GitHub issue does your pull request address?
#123
#113
#106

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

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

No

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.

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

Jo Lynne Rokita added 2 commits September 24, 2020 14:25
- rearrange table order
- add S2 title
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AppVeyor build 1.0.121 for commit 77e9f00 is now complete.

Found 24 potential spelling error(s). Preview:content/03.methods.md:5:CBTN
content/03.methods.md:7:CBTN
content/03.methods.md:9:CBTN
content/03.methods.md:9:CBTN
content/03.methods.md:10:CBTN
content/03.methods.md:11:CBTN
content/03.methods.md:13:CBTN
content/03.methods.md:39:CBTN
content/03.methods.md:58:CBTN
content/03.methods.md:283:CBTN
content/03.methods.md:285:CBTN
content/03.methods.md:300:CBTN
content/03.methods.md:336:Occipital
content/03.methods.md:337:Brai...
The rendered manuscript from this build is temporarily available for download at:

add line about `pathology_diagnosis` and `pathology_free_text_diagnosis` in subtyping section
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AppVeyor build 1.0.122 for commit 320e253 is now complete.

Found 24 potential spelling error(s). Preview:content/03.methods.md:5:CBTN
content/03.methods.md:7:CBTN
content/03.methods.md:9:CBTN
content/03.methods.md:9:CBTN
content/03.methods.md:10:CBTN
content/03.methods.md:11:CBTN
content/03.methods.md:13:CBTN
content/03.methods.md:39:CBTN
content/03.methods.md:58:CBTN
content/03.methods.md:283:CBTN
content/03.methods.md:285:CBTN
content/03.methods.md:300:CBTN
content/03.methods.md:336:Occipital
content/03.methods.md:337:Brai...
The rendered manuscript from this build is temporarily available for download at:

add genes/brain region terms to dictionary
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AppVeyor build 1.0.123

Found 0 potential spelling error(s). Preview:...
for commit db6490b is now complete. The rendered manuscript from this build is temporarily available for download at:

@jharenza jharenza added the ready for review ready for review label Sep 24, 2020
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@jaclyn-taroni jaclyn-taroni left a comment

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Looks good to me! I had one suggestion, but I am not attached to that idea.

add suggestion from review

Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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AppVeyor build 1.0.124 for commit cf9b226 is now complete.

Found 0 potential spelling error(s). Preview:...
The rendered manuscript from this build is temporarily available for download at:

fix two typos
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AppVeyor build 1.0.125 for commit d61ccb5 is now complete.

Found 0 potential spelling error(s). Preview:...
The rendered manuscript from this build is temporarily available for download at:

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3 participants