Published September 25, 2024
| Version v2.4.0
Software
Open
d3b-center/OpenPedCan-analysis: v2.4.0 - Interim module and code updates
Creators
- Jo Lynne Rokita1
- ewafula
- runjin326
- Yuanchao Zhang
- Krutika Gaonkar
- Zhuangzhuang Geng
- Jaclyn Taroni2
- Aditya Lahiri1
- Sangeeta Shukla3
- Komal Rathi1
- Candace Savonen4
- aadamk
- Chante Bethell
- Ryan Corbett1
- Chris Blackden5
- Kelsey Keith
- Joshua Shapiro6
- Casey Greene7
- Yuankun Zhu
- Miguel Brown8
- Alex Sickler
- Dave Hill
- Nhat Duong
- Dan Miller3
- NNoureen
- Bill Amadio9
- Teja Koganti10
- e-t-k11
- afarrel
- yangyangclover
- 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
Files
d3b-center/OpenPedCan-analysis-v2.4.0.zip
Files
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Additional details
Related works
- Is supplement to
- Software: https://github.com/d3b-center/OpenPedCan-analysis/tree/v2.4.0 (URL)