Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / genome-nexus/genome-nexus issues and pull requests

#736 - Add 'Used by' section in documents

Pull Request - State: open - Opened by leexgh 11 months ago

#735 - Add new "Used By" Section in docs

Issue - State: open - Opened by inodb 11 months ago
Labels: documentation

#734 - Handle integrenic variants better

Issue - State: closed - Opened by inodb 11 months ago
Labels: bug, good first issue

#733 - Improve messages in error report

Issue - State: open - Opened by leexgh 11 months ago

#731 - Create automated docker image for annotation-tools

Issue - State: open - Opened by inodb 12 months ago - 1 comment
Labels: enhancement

#730 - Update server to Java 21

Issue - State: open - Opened by leexgh about 1 year ago

#729 - Add grch38 usage document

Pull Request - State: closed - Opened by leexgh about 1 year ago

#728 - Revue parameters should have default value

Issue - State: open - Opened by leexgh about 1 year ago

#727 - GN importer image size too big for github action

Issue - State: closed - Opened by leexgh about 1 year ago

#726 - Update HGNC symbol 202310

Issue - State: closed - Opened by leexgh about 1 year ago

#724 - Annotation pipeline fails when missing variant allele

Issue - State: open - Opened by leexgh about 1 year ago

#723 - MUC3B does not appear in genome nexus

Issue - State: closed - Opened by leexgh about 1 year ago - 1 comment

#722 - Update civic in genome nexus

Issue - State: open - Opened by leexgh about 1 year ago

#721 - Cannot annotate 3:g.28592620T>C

Issue - State: closed - Opened by zhx828 over 1 year ago - 1 comment
Labels: bug

#720 - add alpha fold annotations

Issue - State: open - Opened by inodb over 1 year ago
Labels: enhancement

#718 - Update consequence terms and variant classification

Issue - State: closed - Opened by leexgh over 1 year ago

#717 - wrong default transcript for BRAF in hg38

Issue - State: open - Opened by jjgao over 1 year ago

#716 - VHL misannotation

Issue - State: open - Opened by inodb over 1 year ago - 1 comment
Labels: bug

#715 - New consequence terms and severity order

Pull Request - State: closed - Opened by leexgh over 1 year ago - 1 comment
Labels: enhancement

#714 - Support N allele

Pull Request - State: closed - Opened by leexgh over 1 year ago - 1 comment

#713 - GN frontend indicates invalid hgvsg format but it should not

Issue - State: open - Opened by zhx828 over 1 year ago - 1 comment
Labels: bug, frontend

#712 - Fix docker build test to use multiarch build

Pull Request - State: closed - Opened by inodb over 1 year ago
Labels: test, dependencies

#711 - Specify docker platform

Pull Request - State: closed - Opened by leexgh over 1 year ago

#710 - Support missing end position

Pull Request - State: closed - Opened by leexgh over 1 year ago
Labels: bug

#709 - Add error message for VEP error on POST requests

Pull Request - State: closed - Opened by leexgh over 1 year ago
Labels: enhancement

#707 - Clinvar field name inconsistency

Issue - State: closed - Opened by leexgh over 1 year ago

#706 - Change my variant info clinvar field name

Pull Request - State: closed - Opened by leexgh over 1 year ago
Labels: enhancement

#705 - Update frontend 0831

Pull Request - State: closed - Opened by leexgh over 1 year ago

#704 - Add error message in response for failing annotation

Pull Request - State: closed - Opened by leexgh over 1 year ago - 1 comment

#703 - GRCh37 annotation endpoints return outdated HGNC symbol

Issue - State: open - Opened by leexgh over 1 year ago

#701 - Harmonize genomic location coordinates

Pull Request - State: closed - Opened by leexgh over 1 year ago - 3 comments

#699 - show clinvar version in version API

Issue - State: closed - Opened by inodb over 1 year ago - 2 comments
Labels: enhancement, good first issue

#698 - Update Genome Nexus News

Issue - State: open - Opened by inodb over 1 year ago
Labels: documentation

#696 - Update frontend version

Pull Request - State: closed - Opened by leexgh over 1 year ago

#695 - Specify Reference Assembly When Calling OncoKB API

Pull Request - State: closed - Opened by jeffquinn-msk over 1 year ago
Labels: bug

#694 - Oncokb tests is not working

Issue - State: open - Opened by leexgh over 1 year ago

#693 - Update VUEs.json to be in sync with new reVUE-data repo file

Pull Request - State: closed - Opened by leexgh over 1 year ago - 1 comment

#692 - ClinVar variant is missing in VCF file

Issue - State: closed - Opened by leexgh over 1 year ago

#691 - Fix failing my variant info tests

Pull Request - State: closed - Opened by leexgh over 1 year ago
Labels: test

#690 - My variant info test is failing

Issue - State: open - Opened by leexgh over 1 year ago

#689 - Read reVUE json from reVUE-data repository

Pull Request - State: closed - Opened by leexgh over 1 year ago - 1 comment

#688 - Critical vulnerabilities in genomenexus/gn-mongo:0.27

Issue - State: open - Opened by TJMKuijpers over 1 year ago - 1 comment

#687 - Update oncokb java api client and mapper configs

Pull Request - State: closed - Opened by leexgh over 1 year ago - 5 comments
Labels: bug, dependencies

#686 - Make reVUE JSON URL configurable

Issue - State: open - Opened by inodb over 1 year ago

#685 - Update annotate MAF file link

Pull Request - State: closed - Opened by rmadupuri over 1 year ago

#684 - lollipop plot does not have domain info on grhc38 genome nexus

Issue - State: closed - Opened by inodb almost 2 years ago - 3 comments
Labels: bug

#683 - update docs - add vcf2maf annotation

Pull Request - State: closed - Opened by rmadupuri almost 2 years ago - 2 comments

#682 - CDKN2A multiple transcripts issue

Issue - State: open - Opened by inodb almost 2 years ago

#681 - Fix converting dels using region converter

Pull Request - State: closed - Opened by calvinlu3 almost 2 years ago - 6 comments
Labels: bug

#680 - No VUE return in annotation_summary for revue variants

Issue - State: closed - Opened by leexgh almost 2 years ago
Labels: bug

#679 - Replace reVUE map key

Pull Request - State: closed - Opened by leexgh almost 2 years ago

#678 - OncoKB Annotations Are Not Produced

Issue - State: closed - Opened by jeffquinn-msk almost 2 years ago - 1 comment
Labels: bug

#677 - Create Enum Value for `fields` Parameter of `/annotation` Endpoint, Improve Swagger Doc

Pull Request - State: closed - Opened by jeffquinn-msk almost 2 years ago - 11 comments
Labels: enhancement

#676 - Update needed to solve critical vulnerabilities

Issue - State: open - Opened by TJMKuijpers almost 2 years ago - 2 comments

#675 - Fix Outdated cBioPortal Swagger Endpoint in Notebook Example

Pull Request - State: closed - Opened by jeffquinn-msk almost 2 years ago
Labels: bug

#674 - bug in search field when you add chr in front of the variant

Issue - State: closed - Opened by inodb almost 2 years ago
Labels: bug

#673 - Fix failing insertion annotation with matching alleles

Pull Request - State: closed - Opened by leexgh almost 2 years ago
Labels: bug

#672 - Tests failed because of VUEs.json relative path not accessible

Issue - State: closed - Opened by leexgh almost 2 years ago

#671 - Reading VUEs.json from resources folder

Pull Request - State: closed - Opened by leexgh almost 2 years ago
Labels: test

#670 - Read json file from resources (DO NOT MERGE)

Pull Request - State: closed - Opened by leexgh almost 2 years ago

#669 - Update frontend version

Pull Request - State: closed - Opened by leexgh almost 2 years ago

#668 - TSG pill is not showing for STK11

Issue - State: closed - Opened by inodb almost 2 years ago
Labels: bug

#667 - Add VUEs from Yaeger et al paper

Pull Request - State: closed - Opened by inodb almost 2 years ago

#666 - Reannotate crc_msk_2017 with reVUE

Issue - State: closed - Opened by inodb almost 2 years ago - 1 comment

#665 - Add Oncokb isoform override files

Issue - State: closed - Opened by leexgh almost 2 years ago

#663 - show mskcc transcripts by default on variant page

Issue - State: open - Opened by inodb about 2 years ago
Labels: enhancement

#662 - Error on running genome-nexus-annotation-pipeline

Issue - State: closed - Opened by leexgh about 2 years ago

#661 - Update VUEs.json fields name

Pull Request - State: closed - Opened by leexgh about 2 years ago

#660 - Update frontend

Pull Request - State: closed - Opened by leexgh about 2 years ago

#659 - Copy VUEs.json in dockerfile

Pull Request - State: closed - Opened by leexgh about 2 years ago

#658 - Add reVUE to annotation summary

Pull Request - State: closed - Opened by leexgh about 2 years ago
Labels: enhancement

#657 - reVUE backend integration

Pull Request - State: closed - Opened by aditigopalan about 2 years ago

#656 - reVUE backend integration

Pull Request - State: closed - Opened by aditigopalan about 2 years ago - 1 comment

#655 - ENST00000303806 shows grch38 hgnc symbol H2BC17

Issue - State: open - Opened by leexgh about 2 years ago

#654 - Missing transcripts for H2BC17

Issue - State: closed - Opened by leexgh about 2 years ago - 1 comment
Labels: genome-nexus

#653 - Improve error message

Issue - State: closed - Opened by leexgh about 2 years ago

#652 - Update frontend

Pull Request - State: closed - Opened by leexgh about 2 years ago

#651 - Update frontend version

Pull Request - State: closed - Opened by leexgh about 2 years ago

#650 - No annotation available for 9:g.21974696A>T

Issue - State: open - Opened by zhx828 about 2 years ago - 3 comments
Labels: bug

#649 - Add annotation sources info to 'version' API

Pull Request - State: closed - Opened by leexgh about 2 years ago
Labels: enhancement

#648 - Add annotation sources version info into api

Issue - State: closed - Opened by leexgh about 2 years ago

#642 - Annotation failed 10,89720811,89720811,C,CA

Issue - State: closed - Opened by leexgh over 2 years ago
Labels: bug

#641 - Use docker/build-push-action to build multi-platform images

Pull Request - State: closed - Opened by zhx828 over 2 years ago - 3 comments

#640 - Gene symbols need update

Issue - State: closed - Opened by leexgh over 2 years ago

#628 - Adding index to optimize mutation assessor performance

Pull Request - State: closed - Opened by leexgh over 2 years ago - 1 comment

#617 - Bump gson from 2.3 to 2.8.9 in /service

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#615 - failing to render the lollipop 13:g.32905026_32909888del

Issue - State: closed - Opened by ghost almost 3 years ago - 1 comment

#611 - Add regulatory features

Issue - State: open - Opened by inodb almost 3 years ago - 1 comment
Labels: enhancement

#448 - Mutated Issue: Allele "N" is not being annotated

Issue - State: closed - Opened by yichaoS over 4 years ago - 3 comments
Labels: bug

#447 - Mutated Issue: Annotator jar unable to annotate DNP & TNP variants

Issue - State: open - Opened by yichaoS over 4 years ago - 1 comment

#446 - Mutated Issue: "Splice Region" always get picked as variant class

Issue - State: open - Opened by yichaoS over 4 years ago - 1 comment

#445 - Mutated Issue: Conflicting consequences

Issue - State: closed - Opened by yichaoS over 4 years ago - 1 comment