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Gene.iobio vue

License: MIT License

Vue 49.17% JavaScript 48.13% CSS 1.17% HTML 0.26% Shell 0.21% Sass 1.00% Dockerfile 0.05% Ruby 0.01%

gene.iobio's People

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anderspitman williamrichards2017 adityaekawade bbyun28 metabdel victorfica genostack kchennen whoisdonlee ngslabex eshack94

gene.iobio's Issues

Keep track of last zoom

Allele frequency not annotating correctly on clicked ClinVar variant

In demo WES, click on pathogenic RAI1 variant.

But when clicking on sample variant in ClinVar variants chart, the allele Freq, etc. don't show.

Generic annotations

Exon tooltip - 'Set coverage' link should open FilterSettingsMenu

Add close button for Variants side bar

Preset filters - Add 'settings' button for adding filter, editing filters. Add info to indicate filter is turned on. Add 'Clear filter' button.

Overall progress - Add strobing line when 'Analyze all' running. Add 'Stop analysis' button

After 'unpinning' clicked variant, switching back to variant detail tab shows allele counts only

First, click on a variant. Notices that the variant detail shows correctly.

Now 'Close' the variant in the tooltip. And change to the 'Variant' tab in the 'Genes/Variants' panel. Now only the allele counts appear.

Settings icon in gene description

Selecting the settings just enables choosing the gene source (refseq or gencode). Is it worth having the settings icon, or just leaving the source dropdown in view at all times?

Should counts on filter badges by variant or gene count?

Scroll button for variant detail

Automated tests

Tooltips over gene count badges

Cache - don't prompt user to delete cache

Edu tour sample label needs to be display name (e.g. Jimmy)

Show 'Proband/Mother/Father' in label for each Variant Card

Sample dropdown - need typeahead

Chrome Bug (iobio.js Blob not yet supported) - Marti Tristani

After user clicks on a variant, clicking anywhere outside of the chart should 'unpin' the variant.

Library for components

Export vcf

During 'Analyze all', Variant card shows loading message each time a gene in the list is analyzed

Files dialog - automatics select sample if file has only one

Select gene badge filter should be removed after new gene entered

Distinguish between suggested vs flagged variants

Fix set url when new genes entered

Why isn't phenotype type-ahead alphabetized?

Phenolyzer credit

Refine sorting of Genes in Flagged Variants panel to order by variants rather than dangerSummary

Phenolyzer search - forceSelect vue.js bug

In genes menu, add clear all genes. Init genes in copy/paste to active genes

Only show 'present in affected' row if there are affected sibs or parent, same for unaffected

Consider annotating with dbNSFP tool to get useful Meta SVM and Mutation Taster scores for functional predictions of variant. https://www.ncbi.nlm.nih.gov/pubmed/26555599

Guided tours

Fix prompt (currently breaking gene dropdown if 'No' selected

Call variants on demo data/genes. RAI1 showing Compound het for a variant in Mother, not proband

Ranked variants table obscured in mobile view

X-linked - Do we need gender?

Scoped styles

New screencast

Show links to NCBI, OMIM, GTex in Gene Summary panel

Can't start

After I clone, npm install, and npm start I get the following error

ERROR in ./~/babel-loader/lib!./~/vue-loader/lib/selector.js?type=script&index=0!./client/app/components/partials/Navigation.vue
Module not found: Error: Can't resolve '../../../dist/genes.json' in '/Users/chase/Code/playground/gene.iobio.vue/client/app/components/partials'
 @ ./~/babel-loader/lib!./~/vue-loader/lib/selector.js?type=script&index=0!./client/app/components/partials/Navigation.vue 82:0-48
 @ ./client/app/components/partials/Navigation.vue
 @ ./~/babel-loader/lib!./~/vue-loader/lib/selector.js?type=script&index=0!./client/app/components/pages/Home.vue
 @ ./client/app/components/pages/Home.vue
 @ ./client/app/routes.js
 @ multi ./client/app/routes.js

It looks like the build script is deleting gene.json from the client/dist directory.