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Project description
IDeRare-Pheno
IDeRare or "Indonesia Exome Rare Disease Variant Discovery Pipeline" is simple and ready to use variant discovery pipeline to discover rare disease variants from exome sequencing data.
Quick links
- Documentation
- PyPI Package
- License
- Interactive Webapps Implementation of at Streamlit
What does it do?
This script is recommended if you would like to do conversion, linkage analysis, similarity scoring, and gene-disease recommendation based on the phenotype data provided at clinical_data.txt. Full feature :
- Convert the phenotype data to HPO code (accept mixed SNOMED, LOINC, and HPO code)
- Similarity scoring of differential diagnosis
- Linkage analysis of differential diagnosis (accept mixed SNOMED, ICD-10, ORPHA, OMIM code), include dendrogram tree visualization.
- This should help clinician to systematically doing work-up and excluding similar diagnosis together based on the patient's phenotype.
- Gene and disease recommendation based on the phenotype data similarity scoring between phenotype and OMIM gene and disease databank.
- Linkage analysis of recommended causative gene and disease based on phenotype data (include dendrogram tree visualization).
- This should help clinician to explore / enrich their differential diagnosis based on the patient's phenotype.
- Example of the clinical data provided at Clinical Information Example section
Installation
iderare-pheno requires Python 3.8 or later.
Installing with pip
iderare-pheno is available on PyPI. Just run
pip install iderare-pheno
Installing from source
To install iderare-pheno from source, first clone the repository:
git clone https://github.com/ivanwilliammd/iderare-pheno.git
cd iderare_pheno
Then run
pip install -e .
Usage
from iderare_pheno.converter import term2omim, term2orpha, term2hpo, batchconvert
from iderare_pheno.simrec import hpo2omim_similarity, omim_recommendation, hpo2name
from iderare_pheno.utils import linkage_dendrogram, list2tsv
Team
iderare-pheno is developed and maintained by the author(s), To learn more about who specifically contributed to this codebase, see our contributors page.
License
iderare-pheno license is derived from IDeRare
Project details
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