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

v1.13.2

• Suppress OncoKB data fetch errors (#1204)

v1.13.1

• Oncoprint tracks indicating profiled status in queried profiles (#1167)
• Prevent alphabetical searching example queries list (#1177)
• Fix missing modify query button for subset of virtual study (#1176)
• Fix broken CN segments file (#1175)
• Enable searching for germline in protein change column (#1152)
• Open mycancergenome links in separate tab (#1188)
• Fix copy button behavior (#1190)
• Remove semicolon from custom news section (#1194)
• Don't show invalid allele count values e.g. N/A, undefined, -1 in mutations table (#1165)
• Remove dependency on pdb annotation service (use genomenexus.org instead) (#1068)
• Fix genomic overview when it contains . in the filename (#1094)
• Disallow geneless queries (#1207)

v1.13.0

• Query and delete virtual cohorts in the query interface for authenticated portals (#831)
• Fix tooltip arrow position in survival chart (#1051)
• Show germline mutations in oncoprint (#913)
• Fixes for gene sets (not used in public portal yet)
• Typescript 2.7

v1.12.2

• Oncoprint 'not profiled' improvements. We now only consider it N/P if not profiled by any selected profiles, including non-mutation. We show all this information in the tooltip: #1110.
• Similarly don't show a profile in "Not Profiled In" if its already in "Profiled In", this happens e.g. if one sample is and one sample isnt profiled in the same patient. #1150
• Use correct tumor field for OncoKB tumor type. Solves issue oncokb/oncokb#1034