Code

v12 hgg subtyping (10/N) #331

Code

Merged

jharenza merged 247 commits intov12-nbld3b-center/OpenPedCan-analysis:v12-nblfrom v12-hggd3b-center/OpenPedCan-analysis:v12-hggCopy head branch name to clipboardApr 29, 2023

+128,640-80,493

Commits

Commits on Mar 2, 2023

• update hgg for v12

  

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• update README

  

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• update README

  

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• v12 atrt subtyping

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• rework code to one specimen per line

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Commits on Mar 3, 2023

• update LGAT for v12

  

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• update compile v12

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• Merge branch 'v12-epn' into v12-path

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

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• reslove repeated FGFR subtypes strings

  

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• Update analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd

  Show description for 04d0e8b
  

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• run path subtyping

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Commits on Mar 4, 2023

• regenerate results

  

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• update json terms, cell line composition, rerun

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• fix some typos, stopped at script 07

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• adding backticks to non-standard gene symbol variables

  

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Commits on Mar 5, 2023

• major overhaul, reorder subtyping

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• fix typos, rerun

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• update column names

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• fix missing samples missing due to not selecting na cols

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• fix fusion summary path to data dir, not local!

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• rerun all

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Commits on Mar 6, 2023

• fix missing samples with a different tactic

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• rerun

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• add missing pt and sample ids to subtyping table

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Commits on Mar 9, 2023

• Merge branch 'v12-hgg' into v12-atrt

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• Merge branch 'v12-atrt' into v12-lgg

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• Merge branch 'v12-lgg' into v12-path

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• update path

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• Merge branch 'v12-epn' into v12-path

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• update files

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• Merge branch 'v12-nbl' into v12-hgg

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• Merge branch 'v12-hgg' into v12-atrt

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• Merge branch 'v12-atrt' into v12-lgg

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• Merge branch 'v12-lgg' into v12-path

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• initial run of integrate

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• update wildtype of methly subtype exist

  

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• Merge branch 'v12-lgg' of github.com:PediatricOpenTargets/OpenPedCan-analysis into v12-lgg

  

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• update efo mondo file, few cancer groups

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Commits on Mar 19, 2023

• Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

  

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• rerun with updated v12 data release

  

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• Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

  

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• rerun with updated v12 data release

  

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

  

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• rerun with updated v12 data release

  

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Commits on Mar 20, 2023

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

  

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• rerun with updated v12 data release

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun with updated v12 release

  

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Commits on Mar 22, 2023

• rerun with v12 ef-mondo-ncit map

  

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• v12 independent sample lists

  

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Commits on Apr 13, 2023

• use match id, rerun, update 3 samples with discordant subtypes due to tp53

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• update patient with multiple subtypes

  

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• merge v12-nbl

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• re-run the module

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• merge v12-hgg

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• re-run the module

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• merge v12-atrt

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• merge v12-lgg

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• re-run the module

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• merge v12-path

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• re-run the module

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• merge v12-integrate

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• re-run the module

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• update Other tumors (all histiocytic JXG)

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• update SEGA subtype SEGA, To be classified

  

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

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• rerun module

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Commits on Apr 14, 2023

• add missing methyl samples, rerun

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• Merge branch 'v12-hgg' into v12-atrt

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• Merge branch 'v12-atrt' into v12-path

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• rerun with hgg changes

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• Merge branch 'v12-path' into v12-integrate

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• rerun with hgg changes

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• get rid of discrepancies, rerun

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• Merge branch 'v12-hgg' into v12-atrt

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• Merge branch 'v12-atrt' into v12-path

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• add mol subtype methyl in compiled file

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• Merge branch 'v12-path' into v12-integrate

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• include non-subtyped LGG methyl

  

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• include non-subtyped LGG methyl

  

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Commits on Apr 17, 2023

• update 00-ATRT_subtyping.R

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• merge v12-nbl

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• re-run the module

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• merge v12-hgg

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• update scritp and re-run

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• merge v12-atrt

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• merge v12-lgg

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• re-run the module

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• merge v12-path

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• re-run the module

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• merge v12-integrate

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• re-run the module

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Commits on Apr 18, 2023

• update subtyping script to remove duplicates

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• Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

  

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• PR stacking rerun

  

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• Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

  

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

  

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• PR stacking reruns

  

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

  

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• PR stacking reruns

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• PR stacking reruns

  

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• update the subtype script

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• merge v12-atrt

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• Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

  

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• Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

  

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• Merge branch 'v12-atrt' of github.com:PediatricOpenTargets/OpenPedCan-analysis into v12-atrt

  

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

  

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• set unmatched low confidence methyl to NA

  

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

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• set unmatched low confidence methyl to NA

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• set unmatched low confidence methyl to NA

  

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• resolve methyl duplicates

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• resolve methyl duplicates

  

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• add GNT NOS to path dx for gnts

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Commits on Apr 19, 2023

• add GNT NOS to path subtypes --> GNT in subtype

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• Merge branch 'v12-lgg' into v12-path

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• remove NOS from tumors that are have subtypes!

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• get rid of dnets and fix methyl blank subtypes

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• Merge branch 'v12-lgg' into v12-path

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• rerun

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• remove duplicates

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• Merge branch 'v12-path' into v12-integrate

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• remove discrepancies

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• bring in DGD data

  

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

  

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• rerun

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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Commits on Apr 20, 2023

• rerun without DGD samples

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• Merge branch 'v12-lgg' into v12-path

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• Merge branch 'v12-path' into v12-integrate

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• rerun without DGD samples

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• rework LGG using match id

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• Merge branch 'v12-lgg' into v12-path

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• rerun with updated LGG

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• Merge branch 'v12-path' into v12-integrate

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• rerun with LGG update

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• exclude DGD SNV MAF

  

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Commits on Apr 21, 2023

• rerun with new base histologies

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• Update analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd

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• merge v12-hgg

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• rerun without dgd

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• Merge branch 'v12-atrt' into v12-lgg

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• Merge branch 'v12-lgg' into v12-path

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• rerun

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• update cancer group

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• Merge remote-tracking branch 'origin/v12-emb' into v12-path

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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Commits on Apr 25, 2023

• Merge remote-tracking branch 'origin/v12-nbl' into v12-hgg

  

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• rerun with updated pre-release data

  

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• Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

  

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

  

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• rerun with updated pre-release data

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun with updated pre-release data

  

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• Merge remote-tracking branch 'origin/v12-integrate' into v12-independent-samples

  

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• rerun with updated final histologies

  

  Ubuntu

  committed
  1f99842

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• update to compile new epn subtyping file

  

  Ubuntu

  committed
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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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  committed
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• rerun with new compiled epn subtyping file

  

  Ubuntu

  committed
  3de4f91

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• update path dx selection

  jharenza

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• Merge branch 'v12-epn' into v12-path

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• rerun with epn update

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• Merge branch 'v12-path' into v12-integrate

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• rerun hist with epn update

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• fix path dx and free text strings, rerun

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• Merge branch 'v12-hgg' into v12-path

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• rerun with hgg updates for path dx subset

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• Merge branch 'v12-path' into v12-integrate

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• rerun with latest hgg

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• also fix script 02!

  jharenza

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• Merge branch 'v12-hgg' into v12-path

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• rerun with hgg update

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• Merge branch 'v12-path' into v12-integrate

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• update HGG cancer groups

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• rerun with new JSON terms

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• Merge branch 'v12-emb' into v12-path

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• get those last few embryonal stragglers!

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• Merge branch 'v12-emb' into v12-path

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• rerun with updated emb

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• rerun with updated emb

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• one more mixed path dx update in JSON

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• Merge branch 'v12-emb' into v12-path

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• rerun with emb

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• Merge branch 'v12-path' into v12-integrate

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• rerun

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• exclude large input subset files

  

  Ubuntu

  committed
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• rerun with updated pre-release

  

  Ubuntu

  committed
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Commits on Apr 26, 2023

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

  

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

  

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• Merge remote-tracking branch 'origin/v12-chordoma' into v12-ews

  

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  committed
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• rerun with update pre-release data

  

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

  

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

  

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• Merge remote-tracking branch 'origin/v12-chordoma' into v12-ews

  

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• Merge remote-tracking branch 'origin/v12-ews' into v12-emb

  

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• Merge remote-tracking branch 'origin/v12-emb' into v12-neuro

  

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• Merge remote-tracking branch 'origin/v12-neuro' into v12-hgg

  

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• Merge branch 'v12-hgg' of github.com:PediatricOpenTargets/OpenPedCan-analysis into v12-hgg

  

  Ubuntu

  committed
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• rerun with updated pre-release data

  

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  committed
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• Merge remote-tracking branch 'origin/v12-hgg' into v12-atrt

  

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

  

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

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

  Ubuntu

  committed
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• update samples 7316-6047

  

  Ubuntu

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  c14d5c3

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• update samples 7316-6047

  

  Ubuntu

  committed
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• update samples 7316-6047

  

  Ubuntu

  committed
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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

  Ubuntu

  committed
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• update samples 7316-6047

  

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• Merge remote-tracking branch 'origin/v12-integrate' into v12-independent-samples

  

  Ubuntu

  committed
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• rerun with updates final histologies

  

  Ubuntu

  committed
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• v12 CI subset files

  

  Ubuntu

  committed
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Commits on Apr 27, 2023

• update dockerfile to use debian stretch archive

  

  Ubuntu

  committed
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• update molecular-subtyping-MB to run with CI subsets

  

  Ubuntu

  committed
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Commits on Apr 28, 2023

• update subtyping module to run with CI subsets

  

  Ubuntu

  committed
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• update tp53 to run with CI subsets

  

  Ubuntu

  committed
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• Merge pull request #355 from PediatricOpenTargets/v12-subset-files

  Show description for 0c1eb9b
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• exclude immuned deconvo from GA checks

  

  Ubuntu

  committed
  1dd2a39

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Commits on Apr 29, 2023

• Merge pull request #344 from PediatricOpenTargets/v12-independent-samples

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• Merge pull request #336 from PediatricOpenTargets/v12-integrate

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• Merge pull request #335 from PediatricOpenTargets/v12-path

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• Merge pull request #333 from PediatricOpenTargets/v12-lgg

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• Merge pull request #332 from PediatricOpenTargets/v12-atrt

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