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(19/N) Integrate/histology v13 #529

Merged
merged 30 commits into from
Jan 2, 2024
Merged

(19/N) Integrate/histology v13 #529

merged 30 commits into from
Jan 2, 2024

Commits on Dec 30, 2023

  1. pull code from PR506 and rerun

    @jharenza
    jharenza committed Dec 30, 2023
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  2. Merge branch 'path-v13' into int-v13

    @jharenza
    jharenza committed Dec 30, 2023
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  3. rerun

    @jharenza
    jharenza committed Dec 30, 2023
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  4. Merge branch 'path-v13' into int-v13

    @jharenza
    jharenza committed Dec 30, 2023
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  5. rerun after match id fix in path

    @jharenza
    jharenza committed Dec 30, 2023
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  6. fix cg for DHG astrocytoma/gbm/etc

    @jharenza
    jharenza committed Dec 30, 2023
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  7. update 7316-3240 cg and harm dx

    @jharenza
    jharenza committed Dec 30, 2023
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  8. add html

    @jharenza
    jharenza committed Dec 30, 2023
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Commits on Dec 31, 2023

  1. Merge branch 'path-v13' into int-v13

    @jharenza
    jharenza committed Dec 31, 2023
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  2. Merge branch 'path-v13' into int-v13

    @jharenza
    jharenza committed Dec 31, 2023
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  3. Merge branch 'path-v13' into int-v13

    @jharenza
    jharenza committed Dec 31, 2023
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  4. rerun

    @jharenza
    jharenza committed Dec 31, 2023
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  5. fix NA cancer groups

    @jharenza
    jharenza committed Dec 31, 2023
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  6. oops, add back other cgs

    @jharenza
    jharenza committed Dec 31, 2023
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  7. fix a few more NA, add subtype count table

    @jharenza
    jharenza committed Dec 31, 2023
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  8. Independent samples v13

    @jharenza
    jharenza committed Dec 31, 2023
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  9. add chordoma loss samples

    @jharenza
    jharenza committed Dec 31, 2023
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  10. run for v13

    @jharenza
    jharenza committed Dec 31, 2023
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  11. fix appending rnaseq files, chordoma, and add new samples for non gatk

    @jharenza
    jharenza committed Dec 31, 2023
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  12. rerun

    @jharenza
    jharenza committed Dec 31, 2023
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  13. fix typo

    @jharenza
    jharenza committed Dec 31, 2023
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Commits on Jan 1, 2024

  1. add embryonal samples

    @jharenza
    jharenza committed Jan 1, 2024
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  2. change read_rds to readRDS

    @jharenza
    jharenza committed Jan 1, 2024
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  3. test changing perm of rds file

    @jharenza
    jharenza committed Jan 1, 2024
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  4. change back to results dir, add gitignore

    @jharenza
    jharenza committed Jan 1, 2024
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  5. remove turn off subset data option, dir back to scratch, rm gitignore

    @jharenza
    jharenza committed Jan 1, 2024
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Commits on Jan 2, 2024

  1. use match_id

    @jharenza
    jharenza committed Jan 2, 2024
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  2. Merge branch 'indep2-v13' into subset-v13

    @jharenza
    jharenza committed Jan 2, 2024
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  3. Merge pull request #531 from d3b-center/subset-v13 

    (21/21) Subset v13
    @jharenza
    jharenza committed Jan 2, 2024
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  4. Merge pull request #530 from d3b-center/indep2-v13 

    (20/N) Independent specimens v13
    @jharenza
    jharenza committed Jan 2, 2024
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