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