Comments (2)
In particular, there is a de novo variant in gene SPRX that is in the 'slivar prioritized variant'. When gene.iobio is launched with the variant set, this variant shows up under 'filtered variants', meaning it didn't pass any of the standard filters, which is odd, b/c it does seem to pass the 'De novo' filter criteria. Then, if I click on the gene in the genes panel, the variant moves under the 'De novo variants' filter.
You can try this by launching with the 'Tony - troubleshooting SPRX' variant set.
from gene.iobio.
So we know there are a few problems here:
- The filters should be sorted based on the way they are originally ordered on a fresh launch of gene.iobio. This order is not being maintained when launching a saved analysis.
- The 'filtered variants' (variants in variant set, but not passing any of the gene.iobio filters) are getting lost after saving analysis. These variants need to be restored when the saved analysis is launched
- There is an inconsistency in how a variant is passing a filter when launched from a variant set vs when the gene is clicked.
from gene.iobio.
Related Issues (20)
- Move ncbi api key to .env that isn't checked into repo
- Use csi as well as tbi indexes HOT 2
- Refine logic for 'poor' and 'moderate' sequence quality on Variant inspect card. HOT 1
- Remove obsolete code for local vcf and bam files
- Remove obsolete code for SFARI
- Real-time / saved data
- For public gene.iobio, user should be able to save analysis and reload later with quick response times.
- Improve error reporting and show errors, warnings, and info as alerts in Notifications sidebar.
- Introduce transcript card
- Create new screencast based on latest UI and functionality introduced in gene 4.7
- Fix intermittent bug where first variant selected after 'analyze all' completed results in empty set of variants in variants card.
- Rename flagged variants heading 'Filtered variants' and 'Not found' to more descriptive terms
- Maintain consistent order of filters in left hand Variants panel
- In the flagged variants panel, sort the variants alphabetically by gene name within a filter
- Since NCBI eutils on gene fails quite often, don't show as 'warning' in app notifications.
- When a problem is encountered in gene coverage, it is preventing variants from being annotated.
- IGH gene has 2 entries in RefSeq gf
- v4.7.1 Side-panel Bugs (progression and variant numbering) HOT 14
- When viewing the list of transcripts, the xref (gencode<->refseq) field is always blank.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gene.iobio.