Ino de Bruijn
Ino de Bruijn
Try to select a custom list of samples in TCGA Pancan cohort study view: ``` gbm_tcga_pan_can_atlas_2018:TCGA-02-2483-01 ucec_tcga_pan_can_atlas_2018:TCGA-5B-A90C-01 lusc_tcga_pan_can_atlas_2018:TCGA-66-2765-01 brca_tcga_pan_can_atlas_2018:TCGA-A8-A08A-01 brca_tcga_pan_can_atlas_2018:TCGA-AN-A0AL-01 brca_tcga_pan_can_atlas_2018:TCGA-AO-A03V-01 brca_tcga_pan_can_atlas_2018:TCGA-AQ-A04L-01 brca_tcga_pan_can_atlas_2018:TCGA-BH-A203-01 thca_tcga_pan_can_atlas_2018:TCGA-BJ-A0Z0-01 stad_tcga_pan_can_atlas_2018:TCGA-BR-8080-01 stad_tcga_pan_can_atlas_2018:TCGA-CG-4469-01 brca_tcga_pan_can_atlas_2018:TCGA-D8-A13Z-01 lihc_tcga_pan_can_atlas_2018:TCGA-DD-AA3A-01 lihc_tcga_pan_can_atlas_2018:TCGA-ED-A7PX-01 chol_tcga_pan_can_atlas_2018:TCGA-W5-AA2Q-01...
This is the id name that I see here: https://www.cbioportal.org/api/studies/msk_impact_2017/molecular-profiles?direction=ASC&pageNumber=0&pageSize=10000000&projection=SUMMARY
In MSK-IMPACT Cohort: - [ ] Archer results are currently shown as a separate record on the [Patient view](https://cbioportal.mskcc.org/patient?studyId=mskimpact&caseId=P-0037751). Should we leverage the RNA_SUPPORT column and show that column in...
Mutations endpoint no longer needs to do join to check for fusions (this should improve performance)
Would be nice if one could share the URL to a specific pathways viewer (Ndex vs pathwaymapper). E.g. this always goes to pathwaymapper: https://www.cbioportal.org/results/pathways?case_set_id=all&gene_list=PIK3CA&cancer_study_list=5c8a7d55e4b046111fee2296
We can do this work as part ICTR set aside funding. Integrate properly in Genome Nexus TODO: need to make separate epic detailing the set aside work
As reported by @onursumer
On [MSK-IMPACT Cohort](https://beta.cbioportal.mskcc.org/study/summary?id=mskimpact). - [ ] Why are CNA and SV data not 100% profiled? - [ ] Change capitalization `structural variants` -> `Structural Variants` - [x] The SV table...
From user: "The alias endpoint doesn’t seem to work in both directions for gene aliases. For example, if you get aliases for KMT2D it will return MLL2 but if you...