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

New Contributors

• @zzgeng made their first contribution in https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/304
• @migbro made their first contribution in https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/337

Full Changelog: https://github.com/PediatricOpenTargets/OpenPedCan-analysis/compare/v1.1.0...v2.0.0