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PR 1 of 2: Molecular Subtyping - ATRT (Data Prep) #284

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Dec 3, 2019
Merged

PR 1 of 2: Molecular Subtyping - ATRT (Data Prep) #284

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99afccf
Add `ATRT-molecular-subtyping.R` script
cbethell Nov 20, 2019
82eac34
Add markdown displaying heatmaps
cbethell Nov 21, 2019
fc73a44
Update file paths
cbethell Nov 21, 2019
e6724b2
Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysi…
cbethell Nov 22, 2019
9331063
Add `ATRT-molecular-subtyping-plotting.R`
cbethell Nov 22, 2019
8cfc145
Convert pdf plots to png plots
cbethell Nov 22, 2019
db56fa0
Change selection for `reported_gender` to `germline_sex_estimate`
cbethell Nov 25, 2019
b6983a8
Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysi…
cbethell Nov 26, 2019
8e82b94
@jaclyn-taroni suggested changes
cbethell Nov 26, 2019
47b9de8
Remove log2 transformation of ssGSEA data
cbethell Nov 26, 2019
6128430
Update comment and remove unused custom function in `02` plotting script
cbethell Nov 26, 2019
cc1bdc5
Prep and save matrix and annotation files for heatmap
cbethell Nov 27, 2019
b986565
Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysi…
cbethell Nov 28, 2019
3679217
Load in `ComplexHeatmap` library and add `sessionInfo`
cbethell Nov 28, 2019
1238c90
Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysi…
cbethell Dec 2, 2019
4e19a78
Use v11 files
cbethell Dec 2, 2019
130faa3
Merge branch 'master' into atrt-molecular-subtyping
cbethell Dec 2, 2019
ba4936a
Merge remote-tracking branch 'upstream/master' into atrt-molecular-su…
jaclyn-taroni Dec 3, 2019
fe685aa
Various fixes; rerun
jaclyn-taroni Dec 3, 2019
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4 changes: 4 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -105,6 +105,10 @@ jobs:
- run:
name: Tumor mutation burden with TCGA
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/tmb-compare-tcga/compare-tmb.Rmd', clean = TRUE)"

- run:
name: Molecular Subtyping - ATRT
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/molecular-subtyping-ATRT/01-ATRT-molecular-subtyping-data-prep.Rmd', clean = TRUE)"

################################
#### Add your analysis here ####
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