Published September 25, 2024 | Version v2.4.0
Software Open

d3b-center/OpenPedCan-analysis: v2.4.0 - Interim module and code updates

  • 1. Children's Hospital of Philadelphia
  • 2. @AlexsLemonade
  • 3. The Children's Hospital of Philadelphia
  • 4. Fred Hutchinson Cancer Center
  • 5. D3b Center at CHOP
  • 6. Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation
  • 7. University of Colorado
  • 8. @d3b-center @kids-first
  • 9. Rider University
  • 10. Mayo Clinic
  • 11. UCSC Genomics Institute

Description

What's Changed

  • Add missing samples to tmb calculation files by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/560
  • update R and bioconductor versions by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/568
  • re-org docker file, upgrades by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/572
  • update build token/user and docker packages by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/575
  • ⚰️ Remove pull_request condition from build workflow by @devbyaccident in https://github.com/d3b-center/OpenPedCan-analysis/pull/576
  • move analysis module action by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/571
  • Create workflow to update yaml file for manuscript by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/578
  • Module contribution counts by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/573
  • update branch to dev for contributions yaml job by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/581
  • Collect the list for packages/software version by @zzgeng in https://github.com/d3b-center/OpenPedCan-analysis/pull/579
  • Generate plot/counts for the manuscript by @zzgeng in https://github.com/d3b-center/OpenPedCan-analysis/pull/580
  • Manuscript: Add percentage to pie chart by @zzgeng in https://github.com/d3b-center/OpenPedCan-analysis/pull/583
  • add compiled figure, rerun by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/584
  • Rokita/author template by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/585
  • Update manuscript: Generate tables by @zzgeng in https://github.com/d3b-center/OpenPedCan-analysis/pull/588
  • remove gitignore til GHA works by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/582
  • MB SHH subtyping by @rjcorb in https://github.com/d3b-center/OpenPedCan-analysis/pull/565
  • Rjcorb/569 mb shh umap by @rjcorb in https://github.com/d3b-center/OpenPedCan-analysis/pull/594
  • rerun tables for manuscript by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/596
  • rerun author contributions for biorxiv submission - as of July 9 by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/595
  • CNV consensus w freec wxs by @jharenza in https://github.com/d3b-center/OpenPedCan-analysis/pull/591
  • Previously missing PB subtypes added by @sangeetashukla in https://github.com/d3b-center/OpenPedCan-analysis/pull/601
  • rerun immune-deconv with v15 by @komalsrathi in https://github.com/d3b-center/OpenPedCan-analysis/pull/605
  • Undo cancer_group manual override for select sample_ID as per OPC_566 by @sangeetashukla in https://github.com/d3b-center/OpenPedCan-analysis/pull/600
  • update MB SHH abridged output by @rjcorb in https://github.com/d3b-center/OpenPedCan-analysis/pull/602
  • Manual cancer_group assigned for select sample_id with discordant pathology_diagnosis by @sangeetashukla in https://github.com/d3b-center/OpenPedCan-analysis/pull/610

Full Changelog: https://github.com/d3b-center/OpenPedCan-analysis/compare/v2.3.0...v2.3.1

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d3b-center/OpenPedCan-analysis-v2.4.0.zip

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