Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / Clinical-Genomics/scout issues and pull requests
#4518 - Add link chanjo2 coverage report on gene panel page
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 4 comments
Labels: enhancement, Easy
#4517 - Store demo case file paths as absolute paths
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 12 comments
#4516 - Provide a test for the chanjo2_coverage_report endpoint
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 2 comments
Labels: Easy
#4515 - plugin for variant export
Issue -
State: closed - Opened by parlar 7 months ago
- 3 comments
Labels: question
#4514 - More API pin fix
Pull Request -
State: closed - Opened by dnil 7 months ago
- 3 comments
#4513 - pin/unpin on api with document id only can't make event link now...
Issue -
State: closed - Opened by dnil 7 months ago
Labels: bug
#4512 - Add link to chanjo2 coverage on gene panel page
Issue -
State: closed - Opened by northwestwitch 7 months ago
Labels: enhancement
#4511 - Support for local (private?) IGV tracks
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 5 comments
#4510 - Filtering by 'Qual' on cancer variants page
Issue -
State: open - Opened by cogrho 7 months ago
- 5 comments
Labels: enhancement
#4509 - Support for local IGV tracks
Issue -
State: closed - Opened by northwestwitch 7 months ago
Labels: enhancement
#4508 - Fix search for variants in genes present only in build 38 returning no results
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 3 comments
Labels: Easy, Bugfix
#4507 - Fusion specific fields missing from variantS export
Issue -
State: closed - Opened by dnil 7 months ago
Labels: enhancement
#4506 - hg38 only genes not searchable, at least on fusion page?
Issue -
State: closed - Opened by dnil 7 months ago
- 1 comment
Labels: bug
#4505 - Loading HGNC gene group loci
Issue -
State: closed - Opened by dnil 7 months ago
Labels: enhancement, Intermediate
#4504 - Redirect on login seems erratic
Issue -
State: open - Opened by dnil 7 months ago
Labels: QualityOfLife
#4503 - Parse genes partial fusion pairs
Pull Request -
State: closed - Opened by dnil 7 months ago
- 8 comments
#4502 - Apply dark mode styling to multi selects rendered by select2
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4501 - Internal disease links in disease table on diagnosis page now opens in new tab
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 5 comments
#4500 - Add accordion to comment box
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4499 - Version 4.79.1 - patch export variants without rankscore
Pull Request -
State: closed - Opened by dnil 7 months ago
- 7 comments
#4498 - Fix bug exporting variants without rank score
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 2 comments
Labels: Easy, Bugfix
#4497 - Display custom annotations also on cancer variant page
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 2 comments
Labels: Easy
#4496 - Rank score key missing when exporting variants triggers crash
Issue -
State: closed - Opened by northwestwitch 7 months ago
Labels: bug
#4495 - Fix visualization of custom annotations on cancer variants pages
Issue -
State: closed - Opened by northwestwitch 7 months ago
- 9 comments
Labels: bug
#4494 - Open link to OMIM/ORPHA from Diagnosis page on new tab
Issue -
State: closed - Opened by dnil 7 months ago
Labels: Easy, Frontend
#4493 - Fix #4491 - case incidental finding tag
Pull Request -
State: closed - Opened by dnil 7 months ago
- 2 comments
Labels: enhancement, Easy
#4492 - Fix #4490 - route document_id var to category view
Pull Request -
State: closed - Opened by dnil 7 months ago
- 3 comments
Labels: Easy
#4491 - Add incidental finding case tag
Issue -
State: closed - Opened by dnil 7 months ago
Labels: enhancement, Easy
#4490 - Route to variant view with document id should end up on expected view
Issue -
State: closed - Opened by dnil 7 months ago
Labels: Refactor
#4489 - Get an alert on caseS page when somebody validates variants you ordered Sanger sequencing for
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 4 comments
#4488 - Minor release 4.79
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 3 comments
#4487 - Fix #4476 - links to SV classification guideline and guide.
Pull Request -
State: closed - Opened by dnil 7 months ago
- 2 comments
Labels: Customer Request, Easy, Frontend
#4486 - Add instructions on how to connect scout to chanjo2
Issue -
State: closed - Opened by northwestwitch 7 months ago
Labels: enhancement, docs
#4485 - Amend typo in #4483
Pull Request -
State: closed - Opened by dnil 7 months ago
- 2 comments
Labels: Easy, Bugfix
#4484 - ACMG on report - part two
Pull Request -
State: closed - Opened by dnil 7 months ago
- 1 comment
#4483 - Fix #4480 - show ACMG VUS on general report
Pull Request -
State: closed - Opened by dnil 7 months ago
- 4 comments
Labels: Easy, Bugfix
#4482 - 'Institutes to share cases with' select displays institute names and IDs
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 3 comments
Labels: Customer Request, Easy
#4481 - [obophenotype/human-phenotype-ontology] Release v2024-03-06 - 2024-03-06 Release
Issue -
State: closed - Opened by dnil 7 months ago
- 5 comments
Labels: Task
#4480 - Other commented variant missing from somatic general report?
Issue -
State: closed - Opened by dnil 7 months ago
- 1 comment
Labels: bug
#4479 - Updated Loqusdb table to display information on if current case is the one counted when the observations equals one
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 4 comments
#4478 - Logs for obs_cases
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 2 comments
#4477 - Add Cust no to "Share cases"
Issue -
State: closed - Opened by KickiLagerstedt 7 months ago
- 2 comments
Labels: Customer Request, Easy, QualityOfLife
#4476 - Add link(s) to SV classification guidelines
Issue -
State: closed - Opened by dnil 7 months ago
Labels: enhancement, Customer Request
#4475 - Reroute case no institute
Pull Request -
State: closed - Opened by dnil 7 months ago
- 3 comments
Labels: enhancement
#4474 - Add button for displaying STR variants occurring in the dynamic HPO panel on case page
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 6 comments
Labels: Customer Request, Easy
#4473 - Clinical HPO STRs-button
Issue -
State: closed - Opened by SofieCMD 7 months ago
- 1 comment
Labels: enhancement
#4472 - Fix orpha phenomodels
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 4 comments
#4471 - Fix #4470 - add sniffles and cnvpytor
Pull Request -
State: closed - Opened by dnil 7 months ago
- 2 comments
Labels: Easy
#4470 - Add a few LRS callers
Issue -
State: closed - Opened by dnil 7 months ago
Labels: enhancement, Easy
#4469 - Parse trgt VCFs for STR variants
Issue -
State: closed - Opened by dnil 7 months ago
- 1 comment
Labels: enhancement, LRS
#4468 - refactoring phenotype to disease
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4467 - Replaced omim_terms where orphaterms were included
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4466 - disease_term genes now include both symbol and id when fetched from api
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4465 - Display common/uncommon/rare on mei variant summary
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 3 comments
Labels: Easy
#4464 - MEI summary frequency badge could be populated
Issue -
State: closed - Opened by dnil 7 months ago
- 2 comments
Labels: enhancement
#4463 - Show MANE functional annotations on variant's summary
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 8 comments
#4462 - Minor release 4.78
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 8 comments
#4461 - Modify variants to display MANE info from Ensembl and not VEP annotations
Pull Request -
State: closed - Opened by northwestwitch 7 months ago
- 16 comments
#4460 - nf-core raredisease - peddy het check
Issue -
State: closed - Opened by dnil 7 months ago
- 3 comments
Labels: enhancement, question, nf-core/raredisease
#4459 - Replace "omim" with "disease" in case page query search and related functions
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4458 - bug? missing manual and omim inheritence
Issue -
State: closed - Opened by Leif-glitch 7 months ago
- 3 comments
Labels: question
#4457 - Add option to search disease_terms in database to diagnosis page
Pull Request -
State: closed - Opened by TereseBo 7 months ago
- 3 comments
#4456 - Gnomad keys
Pull Request -
State: closed - Opened by dnil 8 months ago
- 7 comments
#4455 - Allow document id variant API connect, and improve user cred check when accessing variants
Pull Request -
State: closed - Opened by dnil 8 months ago
- 4 comments
#4454 - Fix #4329 - add XTR to PAR definition
Pull Request -
State: closed - Opened by dnil 8 months ago
- 3 comments
#4453 - API - add a variant
Issue -
State: open - Opened by dnil 8 months ago
Labels: enhancement
#4452 - API - update manual rank
Issue -
State: closed - Opened by dnil 8 months ago
- 1 comment
Labels: enhancement
#4451 - Fix #4157 - add pin API endpoint
Pull Request -
State: closed - Opened by dnil 8 months ago
- 5 comments
#4450 - Display MANE badges on gene pages
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 2 comments
Labels: Easy, Frontend
#4449 - Update Decipher base urls
Pull Request -
State: closed - Opened by dnil 8 months ago
- 3 comments
Labels: Easy, Bugfix
#4448 - Parse and save MANE transcripts info when updating genes in build 38
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 6 comments
Labels: Easy
#4447 - Malformed queries in DECIPHER links for SV variants
Issue -
State: closed - Opened by alkc 8 months ago
- 2 comments
Labels: bug
#4446 - nf-core raredisease VEP 110 parsing
Issue -
State: closed - Opened by dnil 8 months ago
- 6 comments
Labels: enhancement, nf-core/raredisease
#4445 - nf-core raredisease separate MT files
Issue -
State: closed - Opened by dnil 8 months ago
- 4 comments
Labels: enhancement, blocked, nf-core/raredisease
#4444 - Can we add more information for CNVs uploaded to Scout?
Issue -
State: open - Opened by mathiasbio 8 months ago
- 4 comments
Labels: enhancement, Cancer
#4443 - Fix #4442 - do not bring in ORPHA inheritance model to OMIM specific …
Pull Request -
State: closed - Opened by dnil 8 months ago
- 3 comments
#4442 - ORPHA phenotype
Issue -
State: closed - Opened by Leif-glitch 8 months ago
- 5 comments
Labels: bug
#4441 - Fix #4396 - reset default loglevel to INFO
Pull Request -
State: closed - Opened by dnil 8 months ago
- 4 comments
Labels: Easy, QualityOfLife
#4440 - Fix #4435 - add MEI element name to variant page
Pull Request -
State: closed - Opened by dnil 8 months ago
- 2 comments
Labels: Easy, Frontend
#4439 - Changed the cases.utils.remove button x color for better visibility
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 4 comments
Labels: Easy, Frontend
#4438 - Rename Clinical Significance to Germline Classification on multistep ClinVar form
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 3 comments
Labels: Easy, Frontend
#4437 - Fix #4436 - update GitHub Actions
Pull Request -
State: closed - Opened by dnil 8 months ago
- 7 comments
Labels: Easy
#4436 - Outdated actions
Issue -
State: closed - Opened by dnil 8 months ago
Labels: enhancement
#4435 - MEI annotation "Element" should be shown on variant page
Issue -
State: closed - Opened by dnil 8 months ago
Labels: enhancement, QualityOfLife
#4434 - Two new SO terms (`sequence_variant` and `coding_transcript_variant`)
Pull Request -
State: closed - Opened by alkc 8 months ago
- 6 comments
#4433 - Keep beacon and Matchmaker status for reuploaded cases
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 5 comments
Labels: Easy, Bugfix
#4432 - Matchmaker submission data gets erased on case rerun
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: bug
#4431 - Show the CSQ/Function of related MANE transcript in gene summary in variant view
Issue -
State: closed - Opened by alkc 8 months ago
- 2 comments
Labels: enhancement
#4430 - Rename Clinical significance to Germline classification
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: Easy, Frontend, Task
#4429 - Remove diagnosis X a bit hard to find..
Issue -
State: closed - Opened by dnil 8 months ago
Labels: QualityOfLife, Frontend
#4428 - ORPHA term caseS search
Issue -
State: closed - Opened by dnil 8 months ago
Labels: enhancement
#4427 - Avoid having to load all diagnoses before being able to search the one you are interested in
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: QualityOfLife
#4426 - Add option of downloading clinvar submission as .json
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 6 comments
#4425 - Version 4.77
Pull Request -
State: closed - Opened by dnil 8 months ago
- 10 comments
#4421 - Removed log to console
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 3 comments
#4420 - Add clinvar assertion criteria selection
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 5 comments
#4419 - Fix #4418 - report division-by-zero on depth 0
Pull Request -
State: closed - Opened by dnil 8 months ago
- 4 comments
#4418 - ZeroDivisionError: division by zero while loading case report
Issue -
State: closed - Opened by northwestwitch 8 months ago
- 2 comments
Labels: bug
#4417 - Missing SO terms in `scout.constants.so_terms.py`
Issue -
State: closed - Opened by alkc 8 months ago
- 7 comments
Labels: enhancement
#4416 - [obophenotype/human-phenotype-ontology] Release v2024-02-08
Issue -
State: closed - Opened by dnil 8 months ago
- 2 comments
Labels: Task