v1.18.1

cbioportal/cbioportal

• Allow deletion of virtual study on query page (cBioPortal/cbioportal#5297)

For a complete list of all backend commits see:

cBioPortal/cbioportal@v1.18.0...v1.18.1

cbioportal/cbioportal-frontend

• Fix p-Value calculation in scatter plot (cBioPortal/cbioportal#5346)
• Show OncoPrint scrollbar (cBioPortal/cbioportal#5107)
• Show blank cancer types plot if all data is filtered (cBioPortal/cbioportal#4873)
• Mutations Tab move clear filters to top (cBioPortal/cbioportal#5183)
• Show progress component on OncoPrint (#1699)
• Don't show VAF plot when there's no VAF data (cBioPortal/cbioportal#5108)
• OncoKB performance improvements (cBioPortal/cbioportal#5167)
• Allow log scale for certain clinical attributes in plots tab (cBioPortal/cbioportal#4456)
• Performance improvement results page - only query hotspot genes on genomenexus (#1719)
• Re-enable Mutation Assessor (#1717)
• On Mutations Tab reset filter UI is not showing up (cBioPortal/cbioportal#5255)
• Fix resetting of mutation filter state (#1733)
• Fix Network tab download (#1738)
• Use consistent coloring for clinical attributes in study view and oncoprint (cBioPortal/cbioportal#5026)
• Add download PDF to patient view (cBioPortal/cbioportal#4610)
• Show results if incorrect/old study in session (#1757)
• Fix sort by allele freq on patient view (cBioPortal/cbioportal#5047)
• Include OncoKB Level R2 data (cBioPortal/cbioportal#5238)

For a complete list of all frontend commits see: v1.18.0...v1.18.1

v1.18.0

cbioportal/cbioportal:

• Results page has been moved to frontend repo

cbioportal/cbioportal-frontend:

• Results page has been ported to this repo making it part of the single page app. Only the study view page is still in the old architecture
• Support coloring by mutation type in plots tab of results page

v1.17.1

cbioportal/cbioportal:

• Database migration to v2.7.2. See the docs for an explanation of how to migrate. This fixes problems with the migration in v2.7.0 which was part of the 1.17.0 release. This recomputes MUTATION_COUNT and FRACTION_GENOME_ALTERED clinical data.
• Fix issues in the importer to calculate FGA and MUTATION_COUNT (they would in many cases be N/A)

cbioportal/cbioportal-frontend:

• Add gene sets in plots tab (#1432)
• Use max MUTATION_COUNT of all samples for per patient MUTATION_COUNT of OncoPrint (cBioPortal/cbioportal#4974)

v1.17.0

cbioportal/cbioportal:

• upgrade to spring security v5
• database migration to v2.7.0. This moves computed mutation_count and fraction_genome_altered to clinical data instead of having their own tables. See the docs for an explanation of how to migrate. This migration recomputes all mutation counts and fraction genome altered. For our production database it took 5-10m. It will depend on the amount of data you have and the performance of your mysql server.
• Return p and q values for spearman calculation for coexpression
• Show git commit info in /api/info endpoint. This uses the git commit id plugin, which might break your build if you don't compile with the .git folder present. It's easily ignored by running with heroku and public profile mvn -Pheroku,public clean install

cbioportal/cbioportal-frontend:

• Handle mutation count and fraction genome altered as clinical data
• Show p and q values for spearman in coexpression tab

Detailed issues/PRs

• v1.17.0 milestone

v1.16.1

cbioportal/cbioportal:

• Avoid assertion error crash for importer (cBioPortal/cbioportal#4829)
• Redis compatibility fix for download tab of query builder (cBioPortal/cbioportal#4762)

cbioportal/cbioportal-frontend:

• fix data loading order bug on patient view (cBioPortal/cbioportal#4582)
• increase oncoprint clinical track selector height (#1406)
• Fix mutation mapper tool showing no mutations for BRCA1/BRCA2 (#1414)
• Fix expression tab and plots tab coloring issues (#1413)
• Fix profiled in tracks for multiple study query (#1418)
• Increase coexpression dot size (#1419)
• Expression tab styling fixes (#1420, #1438)
• Remove Pearson from coexpression tab (#1439)
• Fix case list issue when all cases list is in other category (#1449)
• Gray nav buttons for genes w no mutations (#1469)
• Fix bug where profiled tracks were appearing when they shouldn't (#1459)

v1.16.0

No frontend changes. Same as release v1.15.1. This release is merely to keep frontend version number in sync with backend.

v1.15.1

Oncoprint fixes/enhancements:

• show gene name in tooltip of merged track (cBioPortal/cbioportal#4493)
• Fix NaN% in clinical attribute selector (cBioPortal/cbioportal#4599)
• Only show clinical legend for altered cases (cBioPortal/cbioportal#4515)
• fix clinical data availability (#1381)
• fix cosmic count (#1384)

Other fixes:

• Fix PDF download (#1371)
• Add OQL banner to tabs that reflect OQL as well (cBioPortal/cbioportal#4595)
• fix PDF survival chart (#1375)
• Move legend to top in plots tab (#1369)
• plots tab filter out N/A data (#1380)
• allow to save png with background (#1382)
• toggle OQL filtering in mutations tab (#1385)
• on mutation mapper tool, only show mutations for the transcript being displayed (#1372)
• CNA and putative driver coloring in expression tab (#1377)

v1.15.0

• Tabs in query page refactored and now part of cbioportal-frontend repo:
  • plots
  • network (inside iframe)
  • bookmarks
  • expression
• Updated MutationMapper tool to connect to Genome Nexus for annotating mutations on the fly
• Total Mutations and Fraction Genome Altered are available in plots tab
• Enhanced clinical attribute selector for Oncoprint, now showing sample counts per attribute

v1.14.1

• Fix oncoprint expression heatmap legend missing: cBioPortal/cbioportal#4584
• Show parenthesized content in OncoKB card: oncokb/oncokb#1274
• Use mutation effect from first OncoKB call: #1318
• Only download requested chromosomes in api-legacy/copynumbersegments endpoint: cBioPortal/cbioportal#4412
• show tick at 0 in enrichments plot (cBioPortal/cbioportal#4379)
• add description to fraction genome altered (cBioPortal/cbioportal#4477)
• Fix description of enrichments tab p-value (cBioPortal/cbioportal#4435)
• oncoprint change methylation heatmap color scale (https://github.com/cBioPortal/cbioportal-frontend/issues/1229)
• Add download options to vulcano plots on enrichments tab (cBioPortal/cbioportal#4381)
• Fix missing uniprot id in mutations tab (cBioPortal/cbioportal#4403)
• Remove extra log calculation for log ratio on enrichments tab (#1261)
• Show overlapping studies warning when selecting pancan studies with other TCGA studies n same cancer type (cBioPortal/cbioportal#4373)

v1.14.0

• New Feature: Merged Gene Tracks in Oncoprint (http://www.cbioportal.org/onco_query_lang_desc.jsp#merged-gene-tracks)
• Co-expression and Enrichment tabs moved to new architecture
• Multi-study query interface: populate case set selection based on sample lists in studies