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
#4415 - Fix show matching partial causatives on variant page
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 2 comments
#4414 - Enhance log output when VEP transcript variant frequency parsing fails
Pull Request -
State: closed - Opened by alkc 8 months ago
- 3 comments
#4413 - GnomAD LOEUF
Pull Request -
State: closed - Opened by dnil 8 months ago
- 9 comments
#4412 - Fix show matching causatives
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 4 comments
#4411 - question on panel version
Issue -
State: closed - Opened by 4WGH 8 months ago
- 4 comments
Labels: question
#4410 - Rename “Comment on clinical significance” to “Comment on classification” in ClinVar variant files
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 3 comments
#4409 - Rename “Clinical significance citations” to “Classification citations” in ClinVar variant files
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 3 comments
#4408 - Connection failure warning when you run scout --help command
Issue -
State: closed - Opened by northwestwitch 8 months ago
- 4 comments
Labels: bug, wontfix
#4407 - Replace schug dependency with requests to schug web
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 4 comments
Labels: Easy, Bugfix, blocked
#4406 - Add more helpful error message when variant frequency parsing fails in `scout.parse.variant.transcript`
Issue -
State: closed - Opened by alkc 8 months ago
- 1 comment
Labels: enhancement, Easy
#4405 - Error while executing scout after a fresh conda installation - ARM processor
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: question, wontfix
#4404 - Attempt at fixing gunicorn boot
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 1 comment
#4403 - Can't deploy newly-built images on cg-vm1 - Gunicorn error. again
Issue -
State: closed - Opened by northwestwitch 8 months ago
- 7 comments
Labels: bug
#4402 - Chanjo2 report for cases with d4 files
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 42 comments
#4401 - Matching causative not shown
Issue -
State: closed - Opened by MUebe 8 months ago
- 4 comments
Labels: bug
#4400 - Block and then refactor submission of somatic variants to ClinVar
Issue -
State: open - Opened by northwestwitch 8 months ago
Labels: enhancement
#4399 - Refactor `build_case()` and `CaseLoader`
Issue -
State: open - Opened by dnil 8 months ago
Labels: Refactor
#4398 - Update command that downloads ORPHA data to include inheritance file
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: enhancement
#4397 - Unable to parse HGNC ID due to presence of 'HGNC:' prefix
Issue -
State: closed - Opened by lfearnley 8 months ago
- 5 comments
Labels: nf-core/raredisease
#4396 - Relax standard output on CLI
Issue -
State: closed - Opened by dnil 8 months ago
Labels: enhancement, QualityOfLife
#4395 - Allow `poorpipe` long read sequencing uploads
Issue -
State: closed - Opened by dnil 8 months ago
- 4 comments
Labels: enhancement, LRS
#4394 - Rename "Clinical significance" to "Germline classification" in ClinVar variant files
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 5 comments
Labels: Bugfix
#4393 - Update css to not display tiny bordered search-input in disease input field in AddClinVar form
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 4 comments
#4392 - Update ClinVar inheritance models according to changed ClinVar API
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 2 comments
Labels: Easy
#4391 - Many breaking changes in the new ClinVar submission sheets
Issue -
State: closed - Opened by northwestwitch 8 months ago
- 2 comments
Labels: bug
#4390 - Somatic mutation isn't accepted any more among the inheritance mechanisms in ClinVar API submission
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: bug
#4388 - Fix remaining relative paths on load
Pull Request -
State: closed - Opened by dnil 8 months ago
- 12 comments
#4387 - Stop supporting ClinVar submission using CSV files and submit only using the API
Issue -
State: open - Opened by northwestwitch 8 months ago
Labels: Future ideas, QualityOfLife, Refactor, Task
#4386 - Fix ClinVar condition IDs format (add prefix in background)
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 3 comments
Labels: Bugfix
#4385 - Wrong condition ID format for ORPHA terms
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: bug
#4384 - Loqusdbapi only in this "case"
Issue -
State: closed - Opened by dnil 8 months ago
Labels: enhancement, Easy, Task
#4383 - Revert style of pinned variants window on case page
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 2 comments
#4382 - Case page pinned vars layout..
Issue -
State: closed - Opened by dnil 8 months ago
- 4 comments
Labels: Frontend
#4381 - Fix diseases associated to partial causatives (style, links)
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 4 comments
Labels: Easy, Frontend
#4380 - Updated styling of case_report to align card contents and headers
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 3 comments
#4379 - Associate ClinVar variants with Orphanet conditions
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 3 comments
Labels: Easy, Bugfix
#4378 - Fix ClinVar associated condition in multistep form to take care of ORPHA terms
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: bug
#4377 - Introduce a super-simple ClinVar multistep validation system and validate associated condition
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 3 comments
Labels: Easy, QualityOfLife
#4376 - Subject id and phenotype groups
Pull Request -
State: closed - Opened by dnil 8 months ago
- 5 comments
#4375 - Partial causatives-associated diseases not visible on case page
Issue -
State: closed - Opened by northwestwitch 8 months ago
Labels: Easy, Frontend
#4374 - ClinVar HPO-terms only rarely possible as condition for the classification
Issue -
State: closed - Opened by dnil 8 months ago
- 3 comments
Labels: enhancement
#4373 - ClinVar submission: warn when not filling disorder
Issue -
State: closed - Opened by dnil 8 months ago
- 4 comments
Labels: enhancement
#4372 - Display ORPHA codes on diagnoses page
Issue -
State: closed - Opened by northwestwitch 8 months ago
- 1 comment
Labels: enhancement
#4371 - Add inheritance to orpha
Pull Request -
State: closed - Opened by TereseBo 8 months ago
- 3 comments
#4370 - Fix number of phenotypes and genes from case diagnoses
Pull Request -
State: closed - Opened by northwestwitch 8 months ago
- 3 comments
Labels: Easy, Bugfix
#4369 - Alamut linkout documentation
Issue -
State: open - Opened by dnil 8 months ago
Labels: enhancement, docs
#4368 - Error while updating genes
Issue -
State: closed - Opened by northwestwitch 8 months ago
- 1 comment
#4367 - Diagnosis HPO and gene count 0..
Issue -
State: closed - Opened by dnil 8 months ago
Labels: bug
#4366 - Some cases don't have the Diagnoses section
Issue -
State: closed - Opened by northwestwitch 9 months ago
- 4 comments
Labels: bug
#4364 - Remove capital letters from descriptions of ClinVar events on case page
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 3 comments
Labels: Easy
#4363 - Update individual's path to .d4 files for an existing case
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 3 comments
Labels: enhancement, Easy
#4362 - Remove the unused no-variants param from load_case cli
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 3 comments
Labels: Easy
#4361 - Associate .d4 files to individuals when loading a case via config file
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: enhancement, Easy
#4360 - Define paths to d4 files for samples on scout load config
Issue -
State: closed - Opened by northwestwitch 9 months ago
#4359 - Fix #3937 - case status tags
Pull Request -
State: closed - Opened by dnil 9 months ago
- 4 comments
#4358 - New minor version 4.76
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 7 comments
#4357 - Add info on the user responsible for adding a variant to a ClinVar submission + add/remove events
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
#4356 - Frontend for orphacodes
Pull Request -
State: closed - Opened by TereseBo 9 months ago
- 8 comments
#4355 - Show user that created a ClinVar submission, when available
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: Easy
#4354 - Genes for orpha disease_terms are now saved as int, matching the format for omim disease_terms
Pull Request -
State: closed - Opened by TereseBo 9 months ago
- 3 comments
Labels: Easy
#4353 - Fix Pop Freq Cancer SV Variants View
Pull Request -
State: closed - Opened by ivadym 9 months ago
- 6 comments
#4352 - Missing BAM files and chromograph
Issue -
State: closed - Opened by Leif-glitch 9 months ago
- 2 comments
#4351 - Allow ClinVar submissions with custom API keys and allow resetting submission ID
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: Easy, QualityOfLife
#4350 - Possibility to reset ClinVar submission ID to None
Issue -
State: closed - Opened by northwestwitch 9 months ago
#4349 - somatic view variantS archive variants filtering
Issue -
State: closed - Opened by dnil 9 months ago
Labels: enhancement, Cancer
#4348 - Fix archived local obs not visible on cancer variantS page
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 4 comments
Labels: Easy, Bugfix
#4347 - Remove unused parameter in server/blueprints/variant/controllers/observations
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: Easy
#4346 - Update diagnosis page
Pull Request -
State: closed - Opened by TereseBo 9 months ago
- 4 comments
#4345 - Sanger feedback
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 4 comments
Labels: Customer Request
#4343 - Fix sumenu icon fa5
Pull Request -
State: closed - Opened by dnil 9 months ago
- 1 comment
#4342 - Enable Cancer SV observations view
Pull Request -
State: closed - Opened by ivadym 9 months ago
- 6 comments
Labels: Bugfix
#4341 - Missing views for Cancer SVs
Issue -
State: closed - Opened by ivadym 9 months ago
- 7 comments
Labels: bug
#4339 - submenu icon gone missing..
Issue -
State: open - Opened by dnil 9 months ago
- 1 comment
#4338 - GnomAD 38 v4 links
Pull Request -
State: closed - Opened by dnil 9 months ago
- 2 comments
#4337 - Fix removing the same ClinVar variant from 2 different tabs
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: Bugfix
#4336 - Fix None search as default case search in cases form
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 6 comments
Labels: Easy, Bugfix
#4335 - Empty cases side after clicking "Search"
Issue -
State: closed - Opened by Jakob37 9 months ago
- 3 comments
Labels: duplicate
#4334 - Gnomad link to point to v4 for SNVs
Issue -
State: closed - Opened by Jakob37 9 months ago
- 2 comments
Labels: bug
#4332 - New HPO release 2024-01-11
Issue -
State: closed - Opened by northwestwitch 9 months ago
- 5 comments
Labels: Clinical Genomics Solna instance only, Task
#4331 - Loqus DB links to homozygous cases
Issue -
State: open - Opened by Jakob37 9 months ago
- 2 comments
Labels: enhancement, Intermediate
#4329 - Add XTR region to PAR region definition?
Issue -
State: closed - Opened by dnil 9 months ago
Labels: enhancement
#4328 - question about spliceAI
Issue -
State: open - Opened by 4WGH 9 months ago
- 1 comment
Labels: question
#4327 - Removing variant from clinvar submission crash
Issue -
State: closed - Opened by dnil 9 months ago
- 1 comment
Labels: bug
#4326 - Display user responsible for adding to ClinVar subs on the submission list
Issue -
State: closed - Opened by dnil 9 months ago
- 5 comments
Labels: enhancement, QualityOfLife
#4325 - CaseS search field placeholder does not evaporate when typing in the box..
Issue -
State: open - Opened by dnil 9 months ago
Labels: bug
#4324 - Allow users to add additional API-key
Issue -
State: closed - Opened by dnil 9 months ago
Labels: QualityOfLife
#4323 - Fix #4322 - ClinVar submitters cleared with unpriv saving
Pull Request -
State: closed - Opened by dnil 9 months ago
- 2 comments
Labels: Bugfix
#4322 - Saving institute settings as unprivileged user clears allowed clinvar submitters...
Issue -
State: closed - Opened by dnil 9 months ago
Labels: bug
#4321 - Matching partial causatives view on the variant page
Issue -
State: closed - Opened by dnil 9 months ago
- 2 comments
Labels: bug
#4320 - Cannot chose newly added gene panel
Issue -
State: closed - Opened by ielvers 9 months ago
- 6 comments
Labels: question, Customer Request
#4319 - Validate custom image paths when a case is loaded
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: Easy
#4318 - Customise institute settings to be able to display all cases with a given status
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 3 comments
Labels: Customer Request
#4317 - Fix missing genes, links and functional anno for fusion variants in causatives and verified pages
Pull Request -
State: closed - Opened by northwestwitch 9 months ago
- 2 comments
Labels: Bugfix
#4316 - Fixes needed before implementing orpha codes
Pull Request -
State: closed - Opened by TereseBo 10 months ago
- 3 comments
#4315 - Add REVEL, REVEL rank and SpliceAI scores to causatives and validated pages
Pull Request -
State: closed - Opened by northwestwitch 10 months ago
- 2 comments
#4314 - Round CADD score values on causatives page
Issue -
State: closed - Opened by northwestwitch 10 months ago
#4313 - Gene, variant and functional anno make littlle sense for fusion causatives
Issue -
State: closed - Opened by northwestwitch 10 months ago
#4312 - Fixed missing cryptography lib error with Docker on ARM processor
Pull Request -
State: closed - Opened by northwestwitch 10 months ago
- 3 comments
Labels: Easy, QualityOfLife
#4311 - Add SpliceAI-values and REVEL scores to causatives page
Issue -
State: closed - Opened by northwestwitch 10 months ago
Labels: enhancement, Customer Request
#4310 - Fix missing phenomodels icon
Pull Request -
State: closed - Opened by northwestwitch 10 months ago
- 3 comments
Labels: Easy, Bugfix