Exomiser
BioJava
| Exomiser | BioJava | |
|---|---|---|
| 3 | 2 | |
| 181 | 578 | |
| 0.0% | 0.9% | |
| 8.9 | 8.2 | |
| 12 days ago | 19 days ago | |
| Java | Java | |
| GNU Affero General Public License v3.0 | GNU Lesser General Public License v3.0 only |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Exomiser
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I'm looking for a program to identify disease causing variants in a VCF file
That is not a trivial problem, even when you find a variant that could be causing the phenotype, a lot of evidence and expertise is required to validate that. There is not a single program or platform that can do that for you. But if you want to explore your data, there are VEP and Exomiser tools, but be aware those are not diagnostic tools.
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How to analyze your own raw genetic data for rare diseases/pathogenic markers/worst genes
Enter the Exomiser, an open source cross platform program to analyze your VCF file: https://github.com/exomiser/Exomiser The latest release as of this post is 12.1.0 and can be downloaded here: https://github.com/exomiser/Exomiser/releases/download/12.1.0/exomiser-cli-12.1.0-distribution.zip You also need to download the additional data here except for the hg19.zip: https://data.monarchinitiative.org/exomiser/latest/
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Is there a way to automatically classify variants as pathogenic?
VEP, Exomiser, Gemini, ...
BioJava
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Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo
Here is a cache of valid and invalid FASTQ files for unit tests
https://github.com/biojava/biojava/tree/master/biojava-genom...
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GeneWarrior (DNA sequence manipulation web app) is now open source
Btw. this one is somewhat known: https://biojava.org/
What are some alternatives?
go-feature-flag - GO Feature Flag is a simple, complete and lightweight self-hosted feature flag solution 100% Open Source. 🎛️
JFreeChart - A 2D chart library for Java applications (JavaFX, Swing or server-side).
SonarJava - :coffee: SonarSource Static Analyzer for Java Code Quality and Security
XChart - XChart is a light-weight Java library for plotting data.
android-classyshark - Android and Java bytecode viewer
medusa - A JavaFX library for Gauges
rare-disease-wf - (WIP) best-practices workflow for rare disease
charts - A JavaFX library that contains different kind of charts
DNAnalyzer - Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
LogicNG - The Next Generation Logic Library
TilesFX - A JavaFX library containing tiles that can be used for dashboards.
ChartFx - A scientific charting library focused on performance optimised real-time data visualisation at 25 Hz update rates for data sets with a few 10 thousand up to 5 million data points.