Genophenocorr is a Python library for genotype-phenotype association analysis.
An example of simple genotype-phenotype association analysis
# Load HPO
import hpotk
hpo = hpotk.load_minimal_ontology('http://purl.obolibrary.org/obo/hp.json')
# Load a cohort of phenopackets
from genophenocorr.data import get_toy_cohort
cohort = get_toy_cohort()
# Analyze genotype-phenotype associations
from genophenocorr.analysis import CohortAnalysis
from genophenocorr.constants import VariantEffect
cohort_analysis = CohortAnalysis(cohort, 'NM_1234.5', hpo)
frameshift = cohort_analysis.compare_by_variant_type(VariantEffect.FRAMESHIFT_VARIANT)
print(frameshift)
prints a table with genotype-phenotype correlations:
With frameshift_variant Without frameshift_variant
Count Percent Count Percent p-value
HP:0001166 (Arachnodactyly) 4 30.77% 10 76.92% 0.04718
HP:0001250 (Seizure) 11 84.62% 9 69.23% 0.64472
HP:0001257 (Spasticity) 8 61.54% 9 69.23% 1.00000
Documentation
Check out the User guide and the API reference for more info:
- Stable documentation (last release on
mainbranch) - Latest documentation (bleeding edge, latest commit on
developmentbranch)
1 maintainer
Metadata
1 maintainer
Release files for genophenocorr 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| genophenocorr-0.1.0.tar.gz | 35.7 kB | Without provenance | Details for genophenocorr-0.1.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| genophenocorr-0.1.0-py3-none-any.whl | Python 3 | none | any | Details for genophenocorr-0.1.0-py3-none-any.whl |
Total release size: 78.4 kB
Release files / genophenocorr-0.1.0.tar.gz
| Download URL | genophenocorr-0.1.0.tar.gz |
|---|---|
| Size | 35.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
3479f5c24ab31bd067ce60ef9a81c8a936a089b5cbc736c6f2f6608304914c1c
|
|
BLAKE2b-256 checksum How to use checksums |
39e25908daa92166690481470e5b29408db3ece18e9cfaa7d4153422d1641044
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.6
|
Release files / genophenocorr-0.1.0-py3-none-any.whl
| Download URL | genophenocorr-0.1.0-py3-none-any.whl |
|---|---|
| Size | 42.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
8a0c821b48dd58e39806f017325b367e9599ac2c88105e86c8258fb0c97dedd4
|
|
BLAKE2b-256 checksum How to use checksums |
dfdbf5b7cf611798bfbef83270f1f35ec1164cee3082838b85e3046a109a8889
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.6
|
Security for genophenocorr 0.1.0
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.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
