lobster-genomics
Genomics analysis for VCF and PLINK data with GWAS, QC, and variant annotation capabilities.
Installation
pip install lobster-genomics
Agents
| Agent | Description |
|---|---|
genomics_expert |
Full genomics workflow orchestration including data loading, quality control, GWAS analysis, and variant annotation. |
Services
| Service | Purpose |
|---|---|
| GWASService | Genome-wide association study analysis with linear/logistic regression |
| VariantAnnotationService | Variant functional annotation via Ensembl VEP integration |
| GenomicsQualityService | Comprehensive QC including call rate, MAF, HWE, and heterozygosity |
Features
- Load VCF files (whole genome sequencing) and PLINK files (SNP arrays)
- Comprehensive quality control with configurable thresholds
- Call rate filtering at both sample and variant level
- Minor allele frequency (MAF) filtering for rare variant removal
- Hardy-Weinberg equilibrium testing for genotyping errors
- Heterozygosity outlier detection for sample quality assessment
- Linear and logistic regression GWAS with covariate support
- Lambda GC calculation for population stratification assessment
- Principal component analysis (PCA) for ancestry detection
- Variant functional annotation via Ensembl VEP API
- Manhattan plots and QQ plots for GWAS visualization
- PCA scatter plots colored by phenotype or ancestry
Requirements
- Python 3.12+
- lobster-ai >= 1.0.0
- cyvcf2 (VCF parsing)
- bed-reader (PLINK file support)
- sgkit (GWAS and PCA analysis)
Tier Requirement
This is a premium agent. Access is controlled at runtime via Lobster AI's tier system.
Documentation
Full documentation: docs.omics-os.com/docs/agents/genomics
License
MIT
1 maintainer
Metadata
1 maintainer
Release files for lobster-genomics 1.1.425
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| lobster_genomics-1.1.425.tar.gz | 64.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| lobster_genomics-1.1.425-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 131.2 kB
Release files / lobster_genomics-1.1.425.tar.gz
| Download URL | lobster_genomics-1.1.425.tar.gz |
|---|---|
| Size | 64.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
f7ccea9ba8e4c7c3e336f6417970a170362c60a40754dea0da0a4c8e86cf880b
|
|
BLAKE2b-256 checksum How to use checksums |
c8a715f90439d30aa06014909fd648d281607e1b1f2587a1f742db9da54903f0
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 10, 2026.
Transparency logRelease files / lobster_genomics-1.1.425-py3-none-any.whl
| Download URL | lobster_genomics-1.1.425-py3-none-any.whl |
|---|---|
| Size | 66.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
29d31b5e7985930158f8f55d721f2335d9eb503b5dbda1cbc3164d6629333ef8
|
|
BLAKE2b-256 checksum How to use checksums |
1a26eb66bb86918cd20d03570f8b792b14a0108719b48e998375e9b0807c0213
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 10, 2026.
Transparency log
