GitHub repository: iobio/gene.iobio

Issues:
issue_1057: state: open
title: Look into replacing xhr-stream-dl with a native fetch implementation
user: anderspitman
issue_1056: state: open
title: In the gene typeahead, de-emphasize the gene synonyms to de-clutter the interface. 
user: tonydisera
issue_1055: state: open
title: Unable to load gene.iobio.io tool 
user: LimGal
issue_1054: state: open
title: When genes are copy/pasted first, the left gene panel is blank and user isn't prompted to enter data files to proceed.
user: tonydisera
issue_1053: state: open
title: Remove variant categories in left menu
user: AlistairNWard
issue_1046: state: open
title: The cache is not getting cleared out and these old cache items are possibly getting saved in the analysis payload.
user: tonydisera
issue_1045: state: open
title: Simplify code that specified the URL for the iobio gru backend for gene.iobio launched from Mosaic
user: tonydisera
issue_1041: state: open
title: Fixed selectAll apply immediately
user: YangQi007
issue_1040: state: open
title: Select all applies immediately
user: AlistairNWard
issue_1039: state: open
title: Exons are incorrectly numbered - UTRs should not be treated as separate exon
user: tonydisera
labels: bug: Something isn't working
issue_1038: state: open
title: Simplified the code#1026
user: YangQi007
issue_1036: state: open
title: The mosaic annotations are not updated to reflect the annotations of the selected variant
user: tonydisera
labels: bug: Something isn't working
issue_1031: state: open
title: Buttons don't show in Select Annotations dialog when running clin.iobio.io
user: tonydisera
labels: bug: Something isn't working
issue_1026: state: open
title: For selecting custom annotations, simplify code by removing of unnecessary data fields 
user: tonydisera
issue_1021: state: open
title: Add sort alphabetically button to Genes side panel. 
user: tonydisera
issue_1020: state: open
title: For saved analysis in Mosaic, the variant notes are not saving.
user: tonydisera
issue_1019: state: open
title: Add ability to export selected annotations
user: tonydisera
issue_1018: state: open
title: Save checked annotation when saving analysis so that when it is loaded, the selected annotations show
user: tonydisera
issue_1017: state: open
title: Wrong styling on chip in Variants side panel for gene with Phenolyzer hit
user: tonydisera
issue_1014: state: open
title: Is gnomAD vcf that we use in annotateVariants out-of-date? There is a small difference in counts.
user: tonydisera
issue_1013: state: open
title: Clinvar 'counts' track shows barchart across entire gene when switching from one gene to another
user: tonydisera
labels: bug: Something isn't working
issue_1012: state: open
title: gene.iobio phyloP scores differ from VarSome scores
user: tonydisera
labels: bug: Something isn't working
issue_1000: state: open
title: No allele counts in Nebula
user: AlistairNWard
labels: bug: Something isn't working
Nebula: Recreate on Nebula version of gene.iobio
issue_999: state: open
title: Launch gene.iobio w/o gene, Mosaic doesn't send is_pedigree URL parameter and gene.iobio fails
user: tonydisera
labels: bug: Something isn't working
issue_996: state: open
title: App fails to analyze genes when launched from Mosaic w/o gene, and gene list created from phenolyzer search
user: tonydisera
labels: bug: Something isn't working
issue_981: state: open
title: New analysis mode to skip annotating variants
user: tonydisera
issue_975: state: open
title: Investigate harmonizing vcfanno between calypso and gene.iobio
user: tonydisera
issue_960: state: open
title: Document parent-child component structure of gene and model classes
user: tonydisera
issue_957: state: open
title: Move global JS libraries that are still used to be managed by npm
user: anderspitman
issue_944: state: open
title: Handle retry when annotateVariants times out
user: tonydisera
issue_937: state: open
title: Upgrade gene.iobio to vue-cli (decide if vue.js version 2 or 3)
user: tonydisera
issue_927: state: open
title: In the flagged variants panel, sort the variants alphabetically by gene name within a filter
user: tonydisera
issue_917: state: open
title: Remove obsolete code for SFARI 
user: tonydisera
issue_912: state: open
title: Refine logic for 'poor' and 'moderate' sequence quality on Variant inspect card.
user: tonydisera
issue_905: state: open
title: Move ncbi api key to .env that isn't checked into repo
user: tonydisera
issue_904: state: open
title: Bump minimist, karma, karma-mocha, mocha and mkdirp
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_900: state: open
title: Gene.iobio STTR requirements
user: AlistairNWard
issue_887: state: open
title: Bump express from 4.17.1 to 4.17.3
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_885: state: open
title: Bump qs from 6.5.2 to 6.5.3
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_884: state: open
title: Bump decode-uri-component from 0.2.0 to 0.2.2
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_877: state: open
title: Bump scss-tokenizer and node-sass
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_876: state: open
title: Bump postcss, css-loader and vue-loader
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_872: state: open
title: Bump engine.io and karma
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_870: state: open
title: Bump loader-utils, webpack, extract-text-webpack-plugin and webpack-cli
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_867: state: open
title: Spec out integration with Mosaic
user: AlistairNWard
labels: enhancement: New feature or request
issue_861: state: open
title: Bump socket.io-parser and karma
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_853: state: open
title: There should be more validation to ensure that user selected correct genome build
user: tonydisera
issue_850: state: open
title: Communication features
user: AlistairNWard
issue_849: state: open
title: Update dependencies
user: AlistairNWard
issue_848: state: open
title: Analysis versioning and history
user: AlistairNWard
issue_847: state: open
title: Update API
user: AlistairNWard
issue_845: state: open
title: Real-time / saved data - periodic updates
user: AlistairNWard
issue_840: state: open
title: Use https://github.com/pachterlab/gget to get gene info (e.g. ncbi description, gene aliases, canonical transcript)
user: tonydisera
labels: enhancement: New feature or request
issue_836: state: open
title: Issue with upload and analysis
user: Oppyusa
issue_826: state: open
title: Formalize and publish deployment process for gene.iobio and clin.iobio
user: stefinfection
issue_820: state: open
title: Bump async from 2.6.3 to 2.6.4
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_815: state: open
title: Update api client
user: anderspitman
issue_813: state: open
title: Bump follow-redirects from 1.9.0 to 1.14.8
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_811: state: open
title: Bump ajv from 6.10.2 to 6.12.3
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_810: state: open
title: Bump pathval from 1.1.0 to 1.1.1
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_808: state: open
title: Bump undefsafe from 2.0.2 to 2.0.5
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_792: state: open
title: Bump tar from 4.4.13 to 4.4.18
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_787: state: open
title: Get gene.iobio to build with node 14
user: tonydisera
issue_768: state: open
title: When custom filter has overlapping criteria with existing filter, numbers next to variant in Variants tab are mixed up.
user: tonydisera
issue_766: state: open
title: Bump path-parse from 1.0.6 to 1.0.7
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_738: state: open
title: Bump hosted-git-info from 2.8.5 to 2.8.9
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_737: state: open
title: Bump lodash from 4.17.20 to 4.17.21
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_732: state: open
title: Bump y18n from 3.2.1 to 3.2.2
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_724: state: open
title: Bump elliptic from 6.5.3 to 6.5.4
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_696: state: open
title: Bump ini from 1.3.5 to 1.3.8
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_496: state: open
title: Need to remove old unused code
user: anderspitman
issue_460: state: open
title: Prod build size
user: adityaekawade
issue_228: state: open
title: Set timeout on AnalyzeAll and retry
user: tonydisera