JJ Gao

Support AND logic in Merged Gene Tracks of OQL

2

It's been requested multiple times to have AND logic for OQL and I just bumped into it again. Maybe instead of supporting that between tracks (which might be hard), it's...

Adding mutations, CNA, SV gene charts to study view

17

https://github.com/cBioPortal/cbioportal/issues/6278 addresses pulling gene-level continuous data into study view. Let's also support categorical data, ie. mutations, discrete CNAs, and SVs. A pie chart will be displayed. The slices for CNAs:...

One-side or two-side tests

1

In both the Mutual Exclusivity tab and the Comparison page/tab, we use 1-side Fisher's Exact test. [A user](https://groups.google.com/g/cbioportal/c/WbPzItsK_Vc/m/wlTdzmf3AQAJ) asked us whether a 2-side test is more appropriate. Let's consult statisticians.

Since we have switched from [log4j to slf4j](https://github.com/cBioPortal/cbioportal/commit/d0d0b1f3a75671952ee29913257b26b3453ea235), we should update the documentation too: https://docs.cbioportal.org/deployment/deploy-without-docker/pre-build-steps/#prepare-the-log4jproperties-file

show more labels in lollipop diagram

7

It's hard to resolve overlap when showing multiple labels, but let's give the user the option to have multiple labels so that they can adjust them in other tools such...

Clean up Mutations end point

3

I think it's safe to remove these fields: `fisValue`, `functionalImpactScore`, `linkMsa`, `linkPdb`, `linkXvar`, `refseqMrnaId`. Backend files: - [x] core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java - [x] core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java - [x] core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java - [x] core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java - [x]...

Adding arm-level CNA data

11

Just wanted to capture the idea - this is not a priority. - [x] import the data as generic assay data https://github.com/cBioPortal/datahub/issues/1308 - [x] (implement as part of discrete generic...

Brady et al. The genomic landscape of pediatric acute lymphoblastic leukemia. Nature Genetics. 2022.

1

https://www.nature.com/articles/s41588-022-01159-z - [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklist to the issue tracker - [ ] List information...

Andre et al. Genomics to select treatment for patients with metastatic breast cancer. Nature 2022.

1

https://www.nature.com/articles/s41586-022-05068-3 - [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklist to the issue tracker - [ ] List information...

https://pubmed.ncbi.nlm.nih.gov/35868306/ - [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklist to the issue tracker - [ ] List information...