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v12 epn subtyping (3/N) #324

Merged
merged 369 commits into from
Apr 30, 2023
Merged

v12 epn subtyping (3/N) #324

merged 369 commits into from
Apr 30, 2023
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Apr 13, 2023

  1. merge v12-atrt

    @zzgeng
    zzgeng committed Apr 13, 2023
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  2. merge v12-lgg

    @zzgeng
    zzgeng committed Apr 13, 2023
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  3. re-run the module

    @zzgeng
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  4. merge v12-path

    @zzgeng
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  5. re-run the module

    @zzgeng
    zzgeng committed Apr 13, 2023
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  6. merge v12-integrate

    @zzgeng
    zzgeng committed Apr 13, 2023
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  7. re-run the module

    @zzgeng
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  8. update Other tumors (all histiocytic JXG)

    @jharenza
    jharenza committed Apr 13, 2023
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  9. update SEGA subtype SEGA, To be classified

    Ubuntu committed Apr 13, 2023
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  10. Merge remote-tracking branch 'origin/v12-lgg' into v12-path

    @jharenza
    jharenza committed Apr 13, 2023
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  11. rerun

    @jharenza
    jharenza committed Apr 13, 2023
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  12. Merge branch 'v12-path' into v12-integrate

    @jharenza
    jharenza committed Apr 13, 2023
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  13. rerun module

    @jharenza
    jharenza committed Apr 13, 2023
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Commits on Apr 14, 2023

  1. add missing methyl samples, rerun

    @jharenza
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  2. Merge branch 'v12-hgg' into v12-atrt

    @jharenza
    jharenza committed Apr 14, 2023
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  3. Merge branch 'v12-atrt' into v12-path

    @jharenza
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  4. rerun with hgg changes

    @jharenza
    jharenza committed Apr 14, 2023
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  5. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  6. rerun with hgg changes

    @jharenza
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  7. get rid of discrepancies, rerun

    @jharenza
    jharenza committed Apr 14, 2023
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  8. Merge branch 'v12-hgg' into v12-atrt

    @jharenza
    jharenza committed Apr 14, 2023
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  9. Merge branch 'v12-atrt' into v12-path

    @jharenza
    jharenza committed Apr 14, 2023
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  10. rerun

    @jharenza
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  11. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  12. add mol subtype methyl in compiled file

    @jharenza
    jharenza committed Apr 14, 2023
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  13. Merge branch 'v12-path' into v12-integrate

    @jharenza
    jharenza committed Apr 14, 2023
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  14. include non-subtyped LGG methyl

    Ubuntu committed Apr 14, 2023
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  15. include non-subtyped LGG methyl

    Ubuntu committed Apr 14, 2023
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  16. update 00-subtype script

    @zzgeng
    zzgeng committed Apr 14, 2023
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  17. include non-subtyped EPN methyl

    Ubuntu committed Apr 14, 2023
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  18. update 00-subtype script

    @zzgeng
    zzgeng committed Apr 14, 2023
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  19. include non-subtyped embyronal methyl

    Ubuntu committed Apr 14, 2023
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Commits on Apr 17, 2023

  1. add missing methylation sample

    @zzgeng
    zzgeng committed Apr 17, 2023
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  2. update 00-ATRT_subtyping.R

    @zzgeng
    zzgeng committed Apr 17, 2023
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  3. update 01-neurocytoma-subtyping.Rmd

    @zzgeng
    zzgeng committed Apr 17, 2023
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  4. merge v12-mb

    @zzgeng
    zzgeng committed Apr 17, 2023
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  5. re-run the module

    @zzgeng
    zzgeng committed Apr 17, 2023
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  6. merge v12-epn

    @zzgeng
    zzgeng committed Apr 17, 2023
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  7. re-run the module

    @zzgeng
    zzgeng committed Apr 17, 2023
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  8. merge v12-cranio

    @zzgeng
    zzgeng committed Apr 17, 2023
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  9. merge v12-chordoma

    @zzgeng
    zzgeng committed Apr 17, 2023
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  10. merge v12-ews

    @zzgeng
    zzgeng committed Apr 17, 2023
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  11. include methyl samples

    Ubuntu committed Apr 17, 2023
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  12. merge v12-emb

    @zzgeng
    zzgeng committed Apr 17, 2023
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  13. include methyl samples

    Ubuntu committed Apr 17, 2023
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  14. merge v12-neuro

    @zzgeng
    zzgeng committed Apr 17, 2023
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  15. merge v12-nbl

    @zzgeng
    zzgeng committed Apr 17, 2023
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  16. re-run the module

    @zzgeng
    zzgeng committed Apr 17, 2023
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  17. merge v12-hgg

    @zzgeng
    zzgeng committed Apr 17, 2023
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  18. update scritp and re-run

    @zzgeng
    zzgeng committed Apr 17, 2023
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  19. merge v12-atrt

    @zzgeng
    zzgeng committed Apr 17, 2023
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  20. merge v12-lgg

    @zzgeng
    zzgeng committed Apr 17, 2023
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  21. re-run the module

    @zzgeng
    zzgeng committed Apr 17, 2023
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  22. merge v12-path

    @zzgeng
    zzgeng committed Apr 17, 2023
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  23. re-run the module

    @zzgeng
    zzgeng committed Apr 17, 2023
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  24. merge v12-integrate

    @zzgeng
    zzgeng committed Apr 17, 2023
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  25. re-run the module

    @zzgeng
    zzgeng committed Apr 17, 2023
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Commits on Apr 18, 2023

  1. update subtyping script to remove duplicates

    @zzgeng
    zzgeng committed Apr 18, 2023
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  2. reslove duplicates

    Ubuntu committed Apr 18, 2023
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  3. Merge remote-tracking branch 'origin/v12-epn' into v12-cranio

    Ubuntu committed Apr 18, 2023
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  4. Merge remote-tracking branch 'origin/v12-cranio' into v12-chordoma

    Ubuntu committed Apr 18, 2023
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  5. Merge branch 'v12-chordoma' into v12-ews

    Ubuntu committed Apr 18, 2023
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  6. Merge remote-tracking branch 'origin/v12-ews' into v12-emb

    Ubuntu committed Apr 18, 2023
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  7. stacking rerun

    Ubuntu committed Apr 18, 2023
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  8. Merge remote-tracking branch 'origin/v12-emb' into v12-neuro

    Ubuntu committed Apr 18, 2023
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  9. Merge remote-tracking branch 'origin/v12-neuro' into v12-nbl

    Ubuntu committed Apr 18, 2023
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  10. Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

    Ubuntu committed Apr 18, 2023
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  11. PR stacking rerun

    Ubuntu committed Apr 18, 2023
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  12. Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

    Ubuntu committed Apr 18, 2023
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  13. Merge remote-tracking branch 'origin/v12-atrt' into v12-lgg

    Ubuntu committed Apr 18, 2023
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  14. PR stacking reruns

    Ubuntu committed Apr 18, 2023
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  15. Merge remote-tracking branch 'origin/v12-lgg' into v12-path

    Ubuntu committed Apr 18, 2023
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  16. PR stacking reruns

    Ubuntu committed Apr 18, 2023
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  17. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 18, 2023
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  18. PR stacking reruns

    Ubuntu committed Apr 18, 2023
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  19. update the subtype script

    @zzgeng
    zzgeng committed Apr 18, 2023
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  20. merge v12-atrt

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    zzgeng committed Apr 18, 2023
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  21. set unmatched low confidence methyl to NA

    Ubuntu committed Apr 18, 2023
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  22. Merge remote-tracking branch 'origin/v12-epn' into v12-cranio

    Ubuntu committed Apr 18, 2023
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  23. Merge remote-tracking branch 'origin/v12-cranio' into v12-chordoma

    Ubuntu committed Apr 18, 2023
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  24. Merge remote-tracking branch 'origin/v12-chordoma' into v12-ews

    Ubuntu committed Apr 18, 2023
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  25. set unmatched low confidence methyl to NA

    Ubuntu committed Apr 18, 2023
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  26. Merge remote-tracking branch 'origin/v12-epn' into v12-emb

    Ubuntu committed Apr 18, 2023
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  27. Merge remote-tracking branch 'origin/v12-emb' into v12-neuro

    Ubuntu committed Apr 18, 2023
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  28. Merge remote-tracking branch 'origin/v12-neuro' into v12-nbl

    Ubuntu committed Apr 18, 2023
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  29. set unmatched low confidence methyl to NA

    Ubuntu committed Apr 18, 2023
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  30. Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

    Ubuntu committed Apr 18, 2023
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  31. Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

    Ubuntu committed Apr 18, 2023
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  32. Merge branch 'v12-atrt' of github.com:PediatricOpenTargets/OpenPedCan… 

    …-analysis into v12-atrt
    Ubuntu committed Apr 18, 2023
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  33. Merge remote-tracking branch 'origin/v12-atrt' into v12-lgg

    Ubuntu committed Apr 18, 2023
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  34. set unmatched low confidence methyl to NA

    Ubuntu committed Apr 18, 2023
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  35. Merge remote-tracking branch 'origin/v12-lgg' into v12-path

    Ubuntu committed Apr 18, 2023
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  36. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 18, 2023
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  37. set unmatched low confidence methyl to NA

    Ubuntu committed Apr 18, 2023
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  38. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 18, 2023
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  39. set unmatched low confidence methyl to NA

    Ubuntu committed Apr 18, 2023
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  40. resolve methyl duplicates

    Ubuntu committed Apr 18, 2023
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  41. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 18, 2023
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  42. resolve methyl duplicates

    Ubuntu committed Apr 18, 2023
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  43. add GNT NOS to path dx for gnts

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Commits on Apr 19, 2023

  1. add GNT NOS to path subtypes --> GNT in subtype

    @jharenza
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  2. Merge branch 'v12-lgg' into v12-path

    @jharenza
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  3. remove NOS from tumors that are have subtypes!

    @jharenza
    jharenza committed Apr 19, 2023
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  4. get rid of dnets and fix methyl blank subtypes

    @jharenza
    jharenza committed Apr 19, 2023
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  5. Merge branch 'v12-lgg' into v12-path

    @jharenza
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  6. rerun

    @jharenza
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  7. Merge branch 'v12-path' into v12-integrate

    @jharenza
    jharenza committed Apr 19, 2023
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  8. rerun

    @jharenza
    jharenza committed Apr 19, 2023
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  9. remove duplicates

    @jharenza
    jharenza committed Apr 19, 2023
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  10. Merge branch 'v12-path' into v12-integrate

    @jharenza
    jharenza committed Apr 19, 2023
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  11. remove discrepancies

    @jharenza
    jharenza committed Apr 19, 2023
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  12. bring in DGD data

    Ubuntu committed Apr 19, 2023
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  13. Merge remote-tracking branch 'origin/v12-lgg' into v12-path

    Ubuntu committed Apr 19, 2023
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  14. rerun

    Ubuntu committed Apr 19, 2023
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  15. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 19, 2023
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  16. rerun

    Ubuntu committed Apr 19, 2023
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  17. include DGD samples

    Ubuntu committed Apr 19, 2023
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  18. Merge remote-tracking branch 'origin/v12-emb' into v12-path

    Ubuntu committed Apr 19, 2023
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  19. rerun

    Ubuntu committed Apr 19, 2023
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  20. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 19, 2023
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  21. rerun

    Ubuntu committed Apr 19, 2023
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Commits on Apr 20, 2023

  1. rerun without DGD samples

    @jharenza
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  2. Merge branch 'v12-lgg' into v12-path

    @jharenza
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  3. rerun without DGD samples

    @jharenza
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  4. rerun without DGD samples

    @jharenza
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  5. Merge branch 'v12-path' into v12-integrate

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  6. rerun without DGD samples

    @jharenza
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  7. rework LGG using match id

    @jharenza
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  8. Merge branch 'v12-lgg' into v12-path

    @jharenza
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  9. rerun with updated LGG

    @jharenza
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  10. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  11. rerun with LGG update

    @jharenza
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  12. exclude DGD SNV MAF

    Ubuntu committed Apr 20, 2023
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  13. exclude DGD SNV MAF

    Ubuntu committed Apr 20, 2023
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Commits on Apr 21, 2023

  1. exlcude DGD MAF using updated histologies

    Ubuntu committed Apr 21, 2023
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  2. rerun with new base histologies

    @jharenza
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  3. Update analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd

    @jharenza
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  4. remove commented code

    @jharenza
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  5. merge v12-hgg

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  6. rerun without dgd

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  7. Merge branch 'v12-atrt' into v12-lgg

    @jharenza
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  8. Merge branch 'v12-lgg' into v12-path

    @jharenza
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  9. rerun

    @jharenza
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  10. Merge branch 'v12-path' into v12-integrate

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  11. rerun

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  12. include emb samples not subtyped

    Ubuntu committed Apr 21, 2023
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  13. update cancer group

    @jharenza
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  14. Merge remote-tracking branch 'origin/v12-emb' into v12-path

    Ubuntu committed Apr 21, 2023
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  15. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 21, 2023
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Commits on Apr 23, 2023

  1. remove data table views, move EPN samples to epn-subset

    @jharenza
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  2. refactor classification script

    @jharenza
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  3. add missing methyl samples and rerun

    @jharenza
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Commits on Apr 24, 2023

  1. Merge remote-tracking branch 'origin/v12-mb' into v12-epn

    Ubuntu committed Apr 24, 2023
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  2. Merge remote-tracking branch 'origin/v12-epn' into v12-cranio

    Ubuntu committed Apr 24, 2023
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Commits on Apr 25, 2023

  1. Merge remote-tracking branch 'origin/v12-cranio' into v12-chordoma

    Ubuntu committed Apr 25, 2023
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  2. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  3. Merge remote-tracking branch 'origin/v12-chordoma' into v12-ews

    Ubuntu committed Apr 25, 2023
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  4. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  5. Merge remote-tracking branch 'origin/v12-ews' into v12-emb

    Ubuntu committed Apr 25, 2023
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  6. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  7. Merge remote-tracking branch 'origin/v12-emb' into v12-neuro

    Ubuntu committed Apr 25, 2023
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  8. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  9. Merge remote-tracking branch 'origin/v12-neuro' into v12-nbl

    Ubuntu committed Apr 25, 2023
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  10. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  11. Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

    Ubuntu committed Apr 25, 2023
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  12. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  13. Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

    Ubuntu committed Apr 25, 2023
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  14. Merge remote-tracking branch 'origin/v12-atrt' into v12-lgg

    Ubuntu committed Apr 25, 2023
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  15. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  16. Merge remote-tracking branch 'origin/v12-lgg' into v12-path

    Ubuntu committed Apr 25, 2023
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  17. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  18. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 25, 2023
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  19. rerun with updated pre-release data

    Ubuntu committed Apr 25, 2023
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  20. Merge remote-tracking branch 'origin/v12-integrate' into v12-independ… 

    …ent-samples
    Ubuntu committed Apr 25, 2023
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  21. rerun with updated final histologies

    Ubuntu committed Apr 25, 2023
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  22. update to compile new epn subtyping file

    Ubuntu committed Apr 25, 2023
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  23. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

    Ubuntu committed Apr 25, 2023
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  24. rerun with new compiled epn subtyping file

    Ubuntu committed Apr 25, 2023
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  25. update path dx selection

    @jharenza
    jharenza committed Apr 25, 2023
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  26. Merge branch 'v12-epn' into v12-path

    @jharenza
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  27. rerun with epn update

    @jharenza
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  28. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  29. rerun hist with epn update

    @jharenza
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  30. fix path dx and free text strings, rerun

    @jharenza
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  31. Merge branch 'v12-hgg' into v12-path

    @jharenza
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  32. rerun with hgg updates for path dx subset

    @jharenza
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  33. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  34. rerun with latest hgg

    @jharenza
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  35. also fix script 02!

    @jharenza
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  36. Merge branch 'v12-hgg' into v12-path

    @jharenza
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  37. rerun with hgg update

    @jharenza
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  38. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  39. update HGG cancer groups

    @jharenza
    jharenza committed Apr 25, 2023
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  40. rerun with new JSON terms

    @jharenza
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  41. Merge branch 'v12-emb' into v12-path

    @jharenza
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  42. get those last few embryonal stragglers!

    @jharenza
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  43. Merge branch 'v12-emb' into v12-path

    @jharenza
    jharenza committed Apr 25, 2023
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  44. rerun with updated emb

    @jharenza
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  45. rerun

    @jharenza
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  46. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  47. rerun with updated emb

    @jharenza
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  48. one more mixed path dx update in JSON

    @jharenza
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  49. Merge branch 'v12-emb' into v12-path

    @jharenza
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  50. rerun with emb

    @jharenza
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  51. Merge branch 'v12-path' into v12-integrate

    @jharenza
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  52. rerun

    @jharenza
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  53. exclude large input subset files

    Ubuntu committed Apr 25, 2023
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  54. rerun with updated pre-release

    Ubuntu committed Apr 25, 2023
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Commits on Apr 26, 2023

  1. Merge remote-tracking branch 'origin/v12-epn' into v12-cranio

    Ubuntu committed Apr 26, 2023
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  2. Merge remote-tracking branch 'origin/v12-cranio' into v12-chordoma

    Ubuntu committed Apr 26, 2023
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  3. Merge remote-tracking branch 'origin/v12-chordoma' into v12-ews

    Ubuntu committed Apr 26, 2023
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  4. rerun with update pre-release data

    Ubuntu committed Apr 26, 2023
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  5. Merge remote-tracking branch 'origin/v12-epn' into v12-cranio

    Ubuntu committed Apr 26, 2023
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  6. Merge remote-tracking branch 'origin/v12-cranio' into v12-chordoma

    Ubuntu committed Apr 26, 2023
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  7. Merge remote-tracking branch 'origin/v12-chordoma' into v12-ews

    Ubuntu committed Apr 26, 2023
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  8. Merge remote-tracking branch 'origin/v12-ews' into v12-emb

    Ubuntu committed Apr 26, 2023
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  9. Merge remote-tracking branch 'origin/v12-emb' into v12-neuro

    Ubuntu committed Apr 26, 2023
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  10. Merge remote-tracking branch 'origin/v12-neuro' into v12-hgg

    Ubuntu committed Apr 26, 2023
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  11. Merge branch 'v12-hgg' of github.com:PediatricOpenTargets/OpenPedCan-… 

    …analysis into v12-hgg
    Ubuntu committed Apr 26, 2023
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  12. rerun with updated pre-release data

    Ubuntu committed Apr 26, 2023
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  13. Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

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  14. Merge remote-tracking branch 'origin/v12-atrt' into v12-lgg

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  15. Merge remote-tracking branch 'origin/v12-lgg' into v12-path

    Ubuntu committed Apr 26, 2023
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  16. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

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  17. update samples 7316-6047

    Ubuntu committed Apr 26, 2023
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  18. update samples 7316-6047

    Ubuntu committed Apr 26, 2023
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  19. update samples 7316-6047

    Ubuntu committed Apr 26, 2023
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  20. Merge remote-tracking branch 'origin/v12-path' into v12-integrate

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  21. update samples 7316-6047

    Ubuntu committed Apr 26, 2023
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  22. Merge remote-tracking branch 'origin/v12-integrate' into v12-independ… 

    …ent-samples
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  23. rerun with updates final histologies

    Ubuntu committed Apr 26, 2023
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  24. v12 CI subset files

    Ubuntu committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. update dockerfile to use debian stretch archive

    Ubuntu committed Apr 27, 2023
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  2. update molecular-subtyping-MB to run with CI subsets

    Ubuntu committed Apr 27, 2023
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Commits on Apr 28, 2023

  1. update subtyping module to run with CI subsets

    Ubuntu committed Apr 28, 2023
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  2. update tp53 to run with CI subsets

    Ubuntu committed Apr 28, 2023
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  3. Merge pull request #355 from PediatricOpenTargets/v12-subset-files 

    v12 CI subset files (16/N)
    @jharenza
    jharenza authored Apr 28, 2023
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  4. exclude immuned deconvo from GA checks

    Ubuntu committed Apr 28, 2023
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Commits on Apr 29, 2023

  1. Merge pull request #344 from PediatricOpenTargets/v12-independent-sam… 

    …ples
    @jharenza
    jharenza authored Apr 29, 2023
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  2. Merge pull request #336 from PediatricOpenTargets/v12-integrate

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    jharenza authored Apr 29, 2023
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  3. Merge pull request #335 from PediatricOpenTargets/v12-path

    @jharenza
    jharenza authored Apr 29, 2023
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  4. Merge pull request #333 from PediatricOpenTargets/v12-lgg

    @jharenza
    jharenza authored Apr 29, 2023
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  5. Merge pull request #332 from PediatricOpenTargets/v12-atrt

    @jharenza
    jharenza authored Apr 29, 2023
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  6. Merge pull request #331 from PediatricOpenTargets/v12-hgg

    @jharenza
    jharenza authored Apr 29, 2023
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  7. Merge pull request #330 from PediatricOpenTargets/v12-nbl

    @jharenza
    jharenza authored Apr 29, 2023
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  8. Merge pull request #329 from PediatricOpenTargets/v12-neuro 

    V12 neurocytoma (8/N)
    @jharenza
    jharenza authored Apr 29, 2023
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  9. Merge pull request #328 from PediatricOpenTargets/v12-emb

    @jharenza
    jharenza authored Apr 29, 2023
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  10. Merge pull request #327 from PediatricOpenTargets/v12-ews

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    jharenza authored Apr 29, 2023
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Commits on Apr 30, 2023

  1. Merge pull request #326 from PediatricOpenTargets/v12-chordoma 

    V12 chordoma (5/N)
    @jharenza
    jharenza authored Apr 30, 2023
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  2. Merge pull request #325 from PediatricOpenTargets/v12-cranio

    @jharenza
    jharenza authored Apr 30, 2023
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