https://github.com/rustcodepro/varpred
a variant count approach to predict variant
https://github.com/rustcodepro/varpred
bioinformatics deep-learning machine-learning variant-analysis variants
Last synced: 3 days ago
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a variant count approach to predict variant
- Host: GitHub
- URL: https://github.com/rustcodepro/varpred
- Owner: rustcodepro
- License: mit
- Created: 2025-12-18T08:57:41.000Z (about 1 month ago)
- Default Branch: main
- Last Pushed: 2025-12-18T22:39:16.000Z (about 1 month ago)
- Last Synced: 2025-12-21T22:48:31.473Z (about 1 month ago)
- Topics: bioinformatics, deep-learning, machine-learning, variant-analysis, variants
- Language: Rust
- Homepage:
- Size: 39.1 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# varpred
- a variant count approach to predict variant.
- based on expression values, number of the predicted alt alleles and sequence content.
- Why this:
1. Takes into account the variant associated gene sequence features for machine learning.
2. Any ref allele can have multiple alt allele so convert the alt allele count into a number of the predicted alt allele for feature engineering.
3. Quality value as the input vector and the classification.
4. The ref allele is always a single allele so the frequency of the same.
- This allows you to link the expression of the pathogenic experiment to the predicted variant and classify them to others as pathogenic or not.
- Taking into account all the features including the sequence features ones.
```
cargo build
```
```
variant logistic classifier
************************************************
Gaurav Sablok,
Email: codeprog@icloud.com
************************************************
Usage: varpred
Commands:
classifier Classify a entire population
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
varpred on main is 0.1.0
❯ ./target/debug/varpred classifier -h
Classify a entire population
Usage: varpred classifier
Arguments:
input path to the gtf annotation
input path to the vcf annotation
input path to the expression values
genes fasta file
quality threshold
expression prediction file
threads for the analysis
Options:
-h, --help Print help
```
Gaurav Sablok \
codeprog@icloud.com