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PR 1 of n: Molecular Subtyping - HGG (Defining Lesions) #352

Merged
merged 21 commits into from
Jan 4, 2020
Merged

PR 1 of n: Molecular Subtyping - HGG (Defining Lesions) #352

merged 21 commits into from
Jan 4, 2020

Commits on Dec 18, 2019

  1. Add 01-HGG-molecular-subtyping-data-prep.Rmd 

    - add this analysis to `.circleci`
    @cbethell
    cbethell committed Dec 18, 2019
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  2. Fix command in .circleci

    @cbethell
    cbethell committed Dec 18, 2019
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  3. Merge branch 'master' into hgg-molecular-subtyping-data-prep

    @cbethell
    cbethell authored Dec 18, 2019
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  4. Minor lintr format changes

    @cbethell
    cbethell committed Dec 18, 2019
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  5. Merge branch 'master' into hgg-molecular-subtyping-data-prep

    @cbethell
    cbethell authored Dec 18, 2019
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  6. Log2 transform expression data 

    - rerun notebook
    @cbethell
    cbethell committed Dec 18, 2019
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  7. Merge branch 'master' into hgg-molecular-subtyping-data-prep

    @cbethell
    cbethell authored Dec 18, 2019
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  8. Use controlfreec cn data 

    - rerun notebook
    @cbethell
    cbethell committed Dec 18, 2019
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Commits on Dec 19, 2019

  1. Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysis … 

    …into hgg-molecular-subtyping-data-prep
    @cbethell
    cbethell committed Dec 19, 2019
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  2. Merge branch 'master' into hgg-molecular-subtyping-data-prep

    @jaclyn-taroni
    jaclyn-taroni authored Dec 19, 2019
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  3. Merge branch 'master' into hgg-molecular-subtyping-data-prep

    @cbethell
    cbethell authored Dec 19, 2019
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  4. Merge branch 'hgg-molecular-subtyping-data-prep' of https://github.co… 

    …m/cbethell/OpenPBTA-analysis into hgg-molecular-subtyping-data-prep
    @cbethell
    cbethell committed Dec 19, 2019
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  5. Create a column better distinguishing specific HGG mutations 

    - rerun notebook
    @cbethell
    cbethell committed Dec 19, 2019
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Commits on Jan 3, 2020

  1. Merge branch 'master' of https://github.com/cbethell/OpenPBTA-analysis … 

    …into hgg-molecular-subtyping-data-prep
    @cbethell
    cbethell committed Jan 3, 2020
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  2. Change 01 nb to look only at HGG defining lesions 

    - remove `results/HGG_molecular_subtypes.tsv`
- new output file `results/HGG_defining_lesions.tsv` contains binary columns for all samples distinguishing whether or not they contain any of the four HGG defining lesions
- rename `01` nb to better represent its purpose/content
- rename object `tmb_df` to `snv_df`
    @cbethell
    cbethell committed Jan 3, 2020
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  3. Edit analysis in .circleci to reflect nb name change

    @cbethell
    cbethell committed Jan 3, 2020
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  4. Remove unused lines of code

    @cbethell
    cbethell committed Jan 3, 2020
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  5. Update code to reflect V12 change

    @cbethell
    cbethell committed Jan 3, 2020
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Commits on Jan 4, 2020

  1. Merge branch 'master' into hgg-molecular-subtyping-data-prep

    @jaclyn-taroni
    jaclyn-taroni authored Jan 4, 2020
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  2. Address @jharenza comments

    @jaclyn-taroni
    jaclyn-taroni committed Jan 4, 2020
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  3. Add to modules at a glance table

    @jaclyn-taroni
    jaclyn-taroni committed Jan 4, 2020
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