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Subtype chordoma #475

Merged
merged 27 commits into from
Jan 31, 2020
Merged

Subtype chordoma #475

merged 27 commits into from
Jan 31, 2020

Commits on Nov 21, 2019

  1. Created the README file

    @mkoptyra
    mkoptyra committed Nov 21, 2019
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  2. Copy number- selection of poorly differentiated chordoma (SMARCB1)

    @mkoptyra
    mkoptyra committed Nov 21, 2019
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Commits on Jan 24, 2020

  1. Merge remote-tracking branch 'upstream/master' into subtype-chordoma

    @mkoptyra
    mkoptyra committed Jan 24, 2020
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  2. Updates to the notebook, first graphing attempt

    @mkoptyra
    mkoptyra committed Jan 24, 2020
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  3. updating directory to newer focal_cn file

    @mkoptyra
    mkoptyra committed Jan 24, 2020
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  4. Add notebook to continues integration

    @mkoptyra
    mkoptyra committed Jan 24, 2020
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  5. fixed typo 

    Co-Authored-By: jashapiro <jashapiro@gmail.com>
    @mkoptyra @jashapiro
    mkoptyra and jashapiro authored Jan 24, 2020
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Commits on Jan 25, 2020

  1. Merge remote-tracking branch 'upstream/master' into subtype-chordoma

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  2. Make folder name more consistent with other analyses

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  3. Update directory name in CI

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  4. Use older version of CNVkit file 

    Some style changes
    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  5. Add saving output

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  6. Refresh notebook

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  7. Add more information to the README

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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  8. Add entry to modules at a glance

    @jaclyn-taroni
    jaclyn-taroni committed Jan 25, 2020
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Commits on Jan 30, 2020

  1. Merge remote-tracking branch 'upstream/master' into subtype-chordoma

    @mkoptyra
    mkoptyra committed Jan 30, 2020
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  2. Changes proposed by Jaclyn Taroni ( 

    Making folder name more consistent with other analyses (f270af8)
Updating directory name in CI (2fca75c)
Using older version of CNVkit file (4ded6e8)
Adding saving input (e7c23bd)
Refreshing notebook (5058543)
Adding more information to the README (4ec4aec)
Adding entry to modules at a glance (db258e9 )
    @mkoptyra
    mkoptyra committed Jan 30, 2020
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  3. Plot updated

    @mkoptyra
    mkoptyra committed Jan 30, 2020
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  4. Update analyses/molecular-subtyping-chordoma/01-Subtype-chordoma.Rmd 

    Thank you for the suggestions

Co-Authored-By: jashapiro <jashapiro@gmail.com>
    @mkoptyra @jashapiro
    mkoptyra and jashapiro authored Jan 30, 2020
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  5. Update analyses/molecular-subtyping-chordoma/01-Subtype-chordoma.Rmd 

    Thank you

Co-Authored-By: jashapiro <jashapiro@gmail.com>
    @mkoptyra @jashapiro
    mkoptyra and jashapiro authored Jan 30, 2020
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  6. Update analyses/molecular-subtyping-chordoma/01-Subtype-chordoma.Rmd 

    Co-Authored-By: jashapiro <jashapiro@gmail.com>
    @mkoptyra @jashapiro
    mkoptyra and jashapiro authored Jan 30, 2020
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  7. Minor changes suggested by Josh Shapiro 

    - adding more informative description to some chunks; moving order of the "rm(focal_cn_df)" chunk; editing the graph
    @mkoptyra
    mkoptyra committed Jan 30, 2020
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  8. New graph updated

    @mkoptyra
    mkoptyra committed Jan 30, 2020
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  9. Merge remote-tracking branch 'origin/subtype-chordoma' into subtype-c… 

    …hordoma
    @mkoptyra
    mkoptyra committed Jan 30, 2020
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  10. Fix conflicts in analyses/README

    @jaclyn-taroni
    jaclyn-taroni committed Jan 30, 2020
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  11. Address @jashapiro comments 

    Some minor style changes, updated to use the consensus CN calls
    @jaclyn-taroni
    jaclyn-taroni committed Jan 30, 2020
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  12. Update documentation to indicate that we are using the consensus files

    @jaclyn-taroni
    jaclyn-taroni committed Jan 30, 2020
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