Code

(8/N) EPN v13#518

Code

Merged

jharenza merged 93 commits intomb-v13d3b-center/OpenPedCan-analysis:mb-v13from epn-v13d3b-center/OpenPedCan-analysis:epn-v13Copy head branch name to clipboardJan 2, 2024

+148,248-114,965

Commits

Commits on Dec 30, 2023

• pull code from PR493 and rerun

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  1d0e8e6

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• Merge branch 'mb-v13' into epn-v13

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  a288f32

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• run embryonal subtype for v13

  

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  96a53b3

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• add match id and remove PPTC NBL samples

  

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  acd2b53

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• add code from PR494 and rerun

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  36e0f90

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• pull code from PR495 and rerun

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  b4e4332

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• update gitignore

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  1d61240

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• remove rds file from git

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  0817909

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• update gitignore

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  a288752

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• use match id, rerun with v13

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  3bfdb6f

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• add match id, rerun for v13

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  3813978

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• rerun

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  c5e9746

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• add match_id, run v13

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  40543a8

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• add match id, run pineo v13

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  b255a95

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• rerun

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• pull code from PR500 and rerun:

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• pull code from PR502 and rerun

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• pull code from PR502 and rerun

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• pull code from PR505 and rerun

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• pull code from PR506 and rerun

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  7203b4a

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• Merge branch 'mb-v13' into epn-v13

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  8cedd42

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• Merge branch 'epn-v13' into emb-v13

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• remove MN1--MN1 fusions, as they are in epn/lgg not emb

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• Merge branch 'emb-v13' into chordoma-v13

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  e874761

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• change rds to scratch to fix perm issue, rerun

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  ca4f696

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• Merge branch 'chordoma-v13' into ews-v13

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  c833738

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• Merge branch 'ews-v13' into neuro-v13

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• Merge branch 'neuro-v13' into atrt-v13

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  35b0c91

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• Merge branch 'atrt-v13' into pineo-v13

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• Merge branch 'pineo-v13' into hgg-v13

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  b131f24

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• erge branch 'hgg-v13' into lgg-v13

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• Merge branch 'lgg-v13' into nbl-v13

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• Merge branch 'nbl-v13' into path-v13

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  73353c8

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• rerun

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  254fb14

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• Merge branch 'path-v13' into int-v13

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  d600a0e

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• rerun

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  c166dc5

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• use match id for methyl matching

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  bb4a481

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• Merge branch 'path-v13' into int-v13

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  3b3a42a

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• rerun after match id fix in path

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  183dcac

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• fix cg for DHG astrocytoma/gbm/etc

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  1e46bd2

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• update 7316-3240 cg and harm dx

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  240e0d5

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• add html

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  ebd8f52

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• fix path free text inclusion using grepl

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  b2496c8

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• add specimen list in output

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  0aa5de6

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• Merge branch 'emb-v13' into chordoma-v13

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  8285717

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• Merge branch 'chordoma-v13' into ews-v13

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  04bf6d7

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• Merge branch 'ews-v13' into neuro-v13

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  7a14c3c

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• Merge branch 'neuro-v13' into atrt-v13

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  7e0b629

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• add PPTC samples

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  d1622ca

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• Merge branch 'atrt-v13' into pineo-v13

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  2412563

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• Merge branch 'pineo-v13' into hgg-v13

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• add PPTC to combine table, was missed!

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Commits on Dec 31, 2023

• add EGFR to alterations

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  3d5d4b2

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• Merge branch 'hgg-v13' into lgg-v13

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• Merge branch 'lgg-v13' into nbl-v13

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  bf8e8e2

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• Merge branch 'nbl-v13' into path-v13

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  9d05044

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• rerun

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  dc3ee4c

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• Merge branch 'path-v13' into int-v13

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  e7f531f

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• fix chordoma subtypes adding TBC

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  10f46f6

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• update BS_Q2R56X78, BS_QV60J6XZ, BS_3DV5FVPQ as K28 mut or altered based on manual review of CRAMS

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  4a39283

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• Merge branch 'path-v13' into int-v13

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  b4afd07

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• fix chordoma typo

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  1f9b2fe

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• Merge branch 'path-v13' into int-v13

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  5f4ad65

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• rerun

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  f818d51

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• fix NA cancer groups

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  760b884

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• oops, add back other cgs

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  16c720b

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• fix a few more NA, add subtype count table

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  7c6b1db

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• Independent samples v13

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  ee84c11

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• add chordoma loss samples

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  4840991

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• run for v13

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  0ca563d

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• fix appending rnaseq files, chordoma, and add new samples for non gatk

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  committed
  bfb15d5

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• rerun

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  f20a6ac

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• fix typo

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Commits on Jan 1, 2024

• add embryonal samples

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• change read_rds to readRDS

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  3fe6c7b

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• test changing perm of rds file

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  ac8c778

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• change back to results dir, add gitignore

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  5e083b3

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• remove turn off subset data option, dir back to scratch, rm gitignore

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Commits on Jan 2, 2024

• use match_id

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• Merge branch 'indep2-v13' into subset-v13

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  fe919a2

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• Merge pull request #531 from d3b-center/subset-v13

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• Merge pull request #530 from d3b-center/indep2-v13

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• Merge pull request #529 from d3b-center/int-v13

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• Merge pull request #528 from d3b-center/path-v13

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• Merge pull request #527 from d3b-center/nbl-v13

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• Merge pull request #526 from d3b-center/lgg-v13

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• Merge pull request #525 from d3b-center/hgg-v13

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• Merge pull request #524 from d3b-center/pineo-v13

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• Merge pull request #523 from d3b-center/atrt-v13

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• Merge pull request #522 from d3b-center/neuro-v13

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• Merge pull request #521 from d3b-center/ews-v13

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• Merge pull request #520 from d3b-center/chordoma-v13

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• Merge pull request #519 from d3b-center/emb-v13

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