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Update READMEs #618

Merged
merged 11 commits into from
Mar 10, 2020
Merged

Update READMEs #618

merged 11 commits into from
Mar 10, 2020

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jharenza
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@jharenza jharenza commented Mar 10, 2020

Purpose/implementation Section

What scientific question is your analysis addressing?

NA, updating readme numbers
Updating analysis modules to more clearly define which files are included in the data download
Updated molecular subtype results files for HGG and embryonal tumors

What was your approach?

Whoops - missed this table to update RNA-Seq

clin <- read.delim("~/OpenPBTA-analysis/data/release-v15-20200228/pbta-histologies.tsv", sep = "\t", header = T)
table(clin$experimental_strategy, clin$sample_type)
         Normal Tumor
  Panel        1     1
  RNA-Seq      0  1028
  WGS        801   940
  WXS         31    31

What GitHub issue does your pull request address?

corresponding to latest changes in #543 and #588

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

Which areas should receive a particularly close look?

minor table update
analysis modules readme - double check

Is there anything that you want to discuss further?

No

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

Yes

Jo Lynne Rokita added 9 commits March 9, 2020 20:14
missed this table to update RNA-Seq
add annotation for data download for missed file
update gistic output filename
deduplicate TMB filenames and change them to match release files
This reverts commit df83874.
update filenames for TMB, fix which are in release
@jharenza jharenza requested a review from jaclyn-taroni March 10, 2020 13:46
@jharenza jharenza added the ready for review Used to label pull requests that are ready for review label Mar 10, 2020
@jharenza jharenza changed the title Update README.md Update READMEs Mar 10, 2020
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@jaclyn-taroni
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Documentation only change - merging without CI check.

@jaclyn-taroni jaclyn-taroni merged commit a5d6857 into master Mar 10, 2020
@jaclyn-taroni jaclyn-taroni deleted the update-analysis-readme2 branch March 10, 2020 18:58
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