Onur Sumer

Clinical Data Bin Counts endpoint followup

1

- [ ] Do not query database with sample identifiers, filter in memory instead - [ ] Add a test for dynamic bin calculation

Add new alteration counts endpoint

2

Related to #9305 - Add an endpoint to fetch alteration counts by gene - Request parameters are entrez gene ids, molecular profile case identifiers, and an alteration filter. - Fetching...

IGV 2.0

11

Customize IGV 2.0 to meet Patient and Study pages' needs - [x] https://github.com/cbioportal/cbioportal/issues/5700 - [x] https://github.com/cbioportal/cbioportal/issues/4348 - [x] https://github.com/cbioportal/cbioportal/issues/4411 - [x] https://github.com/cbioportal/cbioportal/issues/4670 - [x] https://github.com/cbioportal/cbioportal/issues/4390 - [ ] https://github.com/cbioportal/cbioportal/issues/4410 -...

Some example pathways: - https://deploy-preview-4338--cbioportalfrontend.netlify.app/comparison/pathways?comparisonId=6133bdcce6ebe01a6ee2cd78 - https://deploy-preview-4338--cbioportalfrontend.netlify.app/comparison/pathways?comparisonId=62dfab908292984755195f62

Issues with alteration frequency and profiled cases counting in the backend

2

1. For genes that are not linked to any gene panel, we use the number of profiled cases for all genes. This does not seem correct, we should only consider...

We use query variables to route to certain static sub tabs. For example: - `comparison_subtab` in [https://www.cbioportal.org/results/comparison?cancer_study_list=ov_tcga_pub...&comparison_subtab=survival](https://www.cbioportal.org/results/comparison?cancer_study_list=ov_tcga_pub&cancer_study_id=ov_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=ov_tcga_pub_mutations&Z_SCORE_THRESHOLD=2.0&case_set_id=ov_tcga_pub_3way_complete&gene_list=BRCA1%20BRCA2&gene_set_choice=user-defined-list&comparison_subtab=survival) - `pathways_source` in [https://www.cbioportal.org/results/pathways?cancer_study_list=ov_tcga_pub...&pathways_source=NDEx](https://www.cbioportal.org/results/pathways?cancer_study_list=ov_tcga_pub&cancer_study_id=ov_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=ov_tcga_pub_mutations&Z_SCORE_THRESHOLD=2.0&case_set_id=ov_tcga_pub_3way_complete&gene_list=BRCA1%20BRCA2&gene_set_choice=user-defined-list&comparison_subtab=survival&pathways_source=NDEx) Ideally we should handle this in the path of...

Currently there is no mechanism to support user defined custom config params/files to customize the frontend IGV component. It would be nice if a user can customize the component by...

Move over the missing functionality from #10265

- Use clinical data counts derived from the new `clinical_data_derived` table instead of fetching all the actual clinical data - Simplify NA count logic. Now NA data is actually in...