v2.4.0 - Interim module and code updates

What's Changed

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

Full Changelog: v2.3.0...v2.3.1

Release v2.3.0

What's Changed

• Run mutational signatures on v13 by @zzgeng in #540
• Pull survival module from OpenPBTA by @jharenza in #547
• Update data-files-description to add miRNA file by @jharenza in #548
• 🐛 Fix Collapse bug by @migbro in #553
• update runs to checkout@v4 to use node20 since node16 is deprecated by @jharenza in #556
• V15 subset files (2/2) by @jharenza in #555
• V15 download and release notes (1/2) by @jharenza in #554

Full Changelog: v2.2.0...v2.3.0

v2.2.0

What's Changed

• Update V13 histologies file README by @jharenza in #535
• Revert "remove figures folder" by @jharenza in #539
• Analysis update: Add methylation in LGAT workflow by @zzgeng in #536
• V14 - subset files (2/2) by @jharenza in #546
• V14 - Rerun Tp53 and molecular subtyping (1/2) by @jharenza in #545

Full Changelog: v2.1.0...v2.2.0

v2.1.0

What's Changed

• remove hardlinking and check from old release in data download script by @jharenza in #358
• update Table S1 - histologies README by @jharenza in #357
• Update to R version 4.2.3 in docker image by @ewafula in #360
• Refactoring molecular-subtyping-ATRT module by @zzgeng in #359
• remove snv consensus module "snv-callers" by @jharenza in #370
• update tmb-calculation README by @ewafula in #371
• Refactoring molecular-subtyping-CRANIO module by @zzgeng in #362
• Refactoring molecular-subtyping-EWS module by @zzgeng in #364
• Refactoring molecular-subtyping-EPN module by @zzgeng in #363
• Refactoring molecular-subtyping-chordoma module by @zzgeng in #366
• Refactoring molecular-subtyping-neurocytoma module by @zzgeng in #365
• Rerun all of the modules with the new docker image by @ewafula in #372
• Add methyl probe annotations liftover process description by @ewafula in #378
• add deconstructSigs v1.9 by @rjcorb in #377
• ⏪ make new temp module for cnv consensus with manta by @sickler-alex in #379
• Updating module per latest v12 successful run on HPC by @sangeetashukla in #381
• 🐛 Fixes bug with GNT in which the broad histology was maintained as LGG instead of GNT by @jharenza in #382
• Include data release process in the repo README by @ewafula in #376
• updated Readme by @atlas4213 in #383
• Update data release analysis process workflow scripts by @ewafula in #380
• Updated analysis: missing NBL samples in histologies file by @zzgeng in #367
• add issue template by @jharenza in #384
• update mutational signatures module by @rjcorb in #300
• Update README.md by @jharenza in #405
• Update CI subset files to include rmats by @ewafula in #406
• Clarify SNV callers included in intersect bed for WGS samples by @ewafula in #408
• Add script to download methyl files by @zzgeng in #415
• Analysis update: remove MTP section from github CI file by @zzgeng in #429
• Updated analysis: copy_number_consensus_call_manta to use only samples which do not have GATK CNV by @zzgeng in #410
• enrich cnv non-GATK samples by @zzgeng in #431
• Create CODEOWNERS by @devbyaccident in #436
• Rerun TMB calculation - test run by @AntoniaChroni in #435
• Analysis update: change LGG methylation subtyping by @zzgeng in #433
• Analysis Update: merge cnv files by @zzgeng in #419
• Analysis update: Reduce docker size by @zzgeng in #440
• Create methyl array probes annotation module by @ewafula in #411
• 👷 Change build and run analysis conditions by @devbyaccident in #445
• Updated analysis: sample 7316-4463 HGG subtyping bug by @zzgeng in #412
• Analysis update: add K28I mutation into subtyping by @zzgeng in #439
• Update analysis: Fix a typo in molecular_subtyping_HGG script by @zzgeng in #446
• Analysis update: Organize Dockerfile and reduce docker size by @zzgeng in #447
• Update focal-cn-file-preparation README by @zzgeng in #457
• Analysis Update: Add neurocytoma workflow to README by @zzgeng in #466
• Analysis Update: Add ATRT subtyping workflow to README by @zzgeng in #467
• Analysis update: Add CRANIO subtyping workflow to README by @zzgeng in #464
• Analysis update: add DMG, EGFR to methyl mol subtype by @zzgeng in #451
• Analysis Update: Add EWS subtyping workflow to README by @zzgeng in #465
• Update analysis: Update age cutoff for CRANIO, PAP by @zzgeng in #472
• Analysis update: Add workflow for HGG molecular subtyping by @zzgeng in #454
• Analysis update: Add NBL workflow to README by @zzgeng in #462
• Analysis update: Add EPN workflow to README by @zzgeng in #461
• Analysis update: Add MB workflow by @zzgeng in #460
• Add workflow to LGG README by @zzgeng in #458
• Analysis update: Add embryonal workflow to README by @zzgeng in #463
• update cancer group by @zzgeng in #453
• add PXA to molecular subtype by @zzgeng in #450
• Change the output format in molecular-subtyping-HGG module by @zzgeng in #374
• New Analysis: add Pineoblastoma subtype module by @zzgeng in #476
• add exclude path diagnosis of PB in EMB subtyping module by @jharenza in #479
• update readmes for deprecated modules, remove unused modules by @jharenza in #481
• update TP53 module/fix HGG discrepancies (2/2) by @jharenza in #478
• V12 subset enrich for samples with TP53 SV (1/2) by @jharenza in #480
• Analysis update: Incorporate the feedback of HOPE non-HGG samples for v13 by @zzgeng in #484
• (21/21) Subset v13 by @jharenza in #531
• (20/N) Independent specimens v13 by @jharenza in #530
• (19/N) Integrate/histology v13 by @jharenza in #529
• (18/N) Pathology v13 by @jharenza in #528
• (17/N) NBL v13 by @jharenza in #527
• (16/N) LGG v13 by @jharenza in #526
• (15/N) HGG v13 by @jharenza in #525
• (14/N) Pineoblastoma v13 by @jharenza in #524
• (13/N) ATRT v13 by @jharenza in #523
• (12/N) Neurocytoma v13 by @jharenza in #522
• (11/N) EWS v13 by @jharenza in #521
• (10/N) Chordoma v13 by @jharenza in #520
• (9/N) Embryonal v13 by @jharenza in #519
• (8/N) EPN v13 by @jharenza in #518
• (6-7/N) MB and CRANIO v13 by @jharenza in #517
• (5/N) TP53 v13 by @jharenza in #516
• (4-D/N) GSVA v13 by @jharenza in #515
• (4-C/N) TMB v13 by @jharenza in #514
• (4-B/N) update and run fusion summary by @jharenza in #513
• (4-A/N) Focal CN v13 by @jharenza in #512
• (3-B/N) GISTIC v13 by @jharenza in #510
• (3-A/N) Indep filt fus v13 by @jharenza in #509
• (...

v2.0.0

This release contains analysis module code and data used for the MTP version 2.0 of the NCI's Pediatric Molecular Targets Platform. Documentation can be found here.

What's Changed

• Update mtp tables qc checks to include expression tpm tables by @adilahiri in #288
• Updated EFO code for Wilms tumor per EFO v45 in prepation for OPC v12… by @sangeetashukla in #272
• update deconstructSigs installation to latest version by @rjcorb in #298
• update generate-mtp-tables.sh by @ewafula in #296
• Create metadata table by @adilahiri in #294
• add mutational signature dependencies to Dockerfile by @rjcorb in #295
• update focal-cn-file-preparation to resolve duplicate status calls by @rjcorb in #292
• update create subset files to enrich for rnaseq batch correction by @ewafula in #297
• Remove pmtl 1 by @sangeetashukla in #290
• Update value formats in the MTP CNV frequencies table by @ewafula in #301
• Updated GSVA module to include cancer_group comparison by @sangeetashukla in #299
• Update focal cn module to gencode v39 by @atlas4213 in #267
• RUVseq RNA Batch Correction by @aadamk in #247
• Update molecular subtyping hgg to gencode v39 by @atlas4213 in #270
• Update tmb calculation module to gencode v39 by @atlas4213 in #269
• update tp53_nfl_score to gencode v39 by @ewafula in #306
• update methylation summary module by @ewafula in #278
• Write batch correct results to scratch folder and delete pilot modules by @ewafula in #309
• Update oncoprint-landscape to use Gencode v39 by @komalsrathi in #308
• 🐛 Data directory should not be cached by @devbyaccident in #312
• Update CI testing data to include methyl matrices and gatk cn subsets by @ewafula in #310
• Update MET fusion by @zzgeng in #304
• Update ATRT subtype by @zzgeng in #311
• Fusion filt bug by @jharenza in #314
• split generate-analysis-files.sh by @ewafula in #313
• Molecular subtyping nbl by @adilahiri in #264
• Update annofuse package and data in dockerfile by @jharenza in #316
• update dockerfile for annofuse by @jharenza in #318
• update fusion-putative-oncogenic.tsv file with annoFuseData by @zzgeng in #317
• Update IHG subtyping by @zzgeng in #305
• Updated analysis: Update mol subtyping integrate to include ATRT + NBL by @zzgeng in #315
• add dasel file format converter to dockerfile by @ewafula in #320
• MTP annotations scripts by @atlas4213 in #319
• Exclude descriptions from MTP disease mapping by @ewafula in #339
• Updated efo-mondo module to use v12 prefill by @sangeetashukla in #342
• Updated input files for gene_match ran the module by @sangeetashukla in #341
• update annotation mygene and refseq datasets by @ewafula in #343
• fusion_filtering duplicates by @kelseykeith in #353
• Updated final codes per discussion on OPC Issue 526 by @sangeetashukla in #350
• v12 cnv and fusion frequencies by @zzgeng in #345
• v12 snv-frequencies by @kelseykeith in #346
• v12 rnaseq expression summary stats by @ewafula in #347
• v12 CI subset files (16/N) by @ewafula in #355
• v12 independent sample lists (15/N) by @ewafula in #344
• V12 mol subtype integrate/create histologies (14/N) by @jharenza in #336
• V12 pathology (13/N) by @jharenza in #335
• v12 lgg subtyping (12/N) by @ewafula in #333
• v12 ATRT subtyping (11/N) by @jharenza in #332
• v12 hgg subtyping (10/N) by @ewafula in #331
• V12 NBL subtyping (9/N) by @jharenza in #330
• V12 neurocytoma (8/N) by @jharenza in #329
• v12 embryonal subtyping (7/N) by @ewafula in #328
• V12 ews (6/N) by @jharenza in #327
• V12 chordoma (5/N) by @jharenza in #326
• Add v12 cranio subtyping (4/N) by @jharenza in #325
• v12 epn subtyping (3/N) by @ewafula in #324
• V12 mb subtyping (2/N) by @jharenza in #322
• v12 release notes by @kelseykeith in #352
• Update v12 pre-release files (1/N) by @ewafula in #321
• ✨ Add liftover and collapse workflow by @migbro in #337
• Bug/mb fix pedcbio sample by @migbro in #354
• Update pre-release data release QC by @ewafula in #334
• Generate mtp tables by @zzgeng in #356
• v12 methylation-summary by @ewafula in #348
• v12-filter-mtp tables by @ewafula in #349
• v12 post data release analyses by @ewafula in #340

New Contributors

• @zzgeng made their first contribution in #304
• @migbro made their first contribution in #337

Full Changelog: v1.1.0...v2.0.0

Release v1.1.0

This release contains analysis module code and data used for the MTP version 1.1 of the NCI's Pediatric Molecular Targets Platform. Documentation can be found here.

Release v1.0.0

This first release contains analysis modules and data used for the first version of the NCI's Pediatric Molecular Targets Platform. Documentation can be found here.