| Name | genophenocorr JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | |
| Summary | Search for genotype-phenotype correlations with GA4GH phenopackets |
| upload_time | 2023-09-28 20:37:07 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.5 |
| license | MIT License Copyright (c) 2023, The Monarch Initiative Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
global alliance for genomics and health
ga4gh phenopacket schema
human phenotype ontology
ga4gh
genotype-phenotype correlation
hpo
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://github.com/monarch-initiative/genophenocorr/actions/workflows/python_ci.yml)
Genophenocorr is a Python library for genotype-phenotype association analysis.
An example of simple genotype-phenotype association analysis
```python
# 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:
```text
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](https://thejacksonlaboratory.github.io/genophenocorr/stable) (last release on `main` branch)
- [Latest documentation](https://thejacksonlaboratory.github.io/genophenocorr/latest) (bleeding edge, latest commit on `development` branch)
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"description": "[](https://github.com/monarch-initiative/genophenocorr/actions/workflows/python_ci.yml)\n\n\n\nGenophenocorr is a Python library for genotype-phenotype association analysis. \n\nAn example of simple genotype-phenotype association analysis\n```python\n# Load HPO\nimport hpotk\nhpo = hpotk.load_minimal_ontology('http://purl.obolibrary.org/obo/hp.json')\n\n# Load a cohort of phenopackets \nfrom genophenocorr.data import get_toy_cohort\ncohort = get_toy_cohort()\n\n# Analyze genotype-phenotype associations \nfrom genophenocorr.analysis import CohortAnalysis\nfrom genophenocorr.constants import VariantEffect\n\ncohort_analysis = CohortAnalysis(cohort, 'NM_1234.5', hpo)\nframeshift = cohort_analysis.compare_by_variant_type(VariantEffect.FRAMESHIFT_VARIANT)\nprint(frameshift)\n```\n\nprints a table with genotype-phenotype correlations:\n\n```text\n With frameshift_variant Without frameshift_variant\n Count Percent Count Percent p-value\nHP:0001166 (Arachnodactyly) 4 30.77% 10 76.92% 0.04718\nHP:0001250 (Seizure) 11 84.62% 9 69.23% 0.64472\nHP:0001257 (Spasticity) 8 61.54% 9 69.23% 1.00000\n```\n\n## Documentation\n\nCheck out the User guide and the API reference for more info:\n\n- [Stable documentation](https://thejacksonlaboratory.github.io/genophenocorr/stable) (last release on `main` branch)\n- [Latest documentation](https://thejacksonlaboratory.github.io/genophenocorr/latest) (bleeding edge, latest commit on `development` branch)\n",
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