Patient phenotype and genotype similarity

This package is research code designed to measure the similarity between patients, using both phenotype (specified as Human Phenotype Ontology terms) and genotype (specified as the Exomiser-processed results of whole-exome VCF files).

Usage example

# Run on example data (expected output in test/test.out)
./patient_similarity.py --log=INFO -s simgic test/test.hpo \
  data/hp.obo data/phenotype_annotation.tab

Name		Name	Last commit message	Last commit date
Latest commit History 89 Commits
data		data
test		test
.gitignore		.gitignore
README.md		README.md
disease.py		disease.py
gene_load.py		gene_load.py
genotype_match_scorer.py		genotype_match_scorer.py
hpo.py		hpo.py
hpo_lookup.py		hpo_lookup.py
hpoic.py		hpoic.py
is_same_cohort.py		is_same_cohort.py
match_scorer.py		match_scorer.py
matrixify.py		matrixify.py
orphanet.py		orphanet.py
patient.py		patient.py
patient_breakdown.py		patient_breakdown.py
patient_ic.py		patient_ic.py
patient_similarity.py		patient_similarity.py
plot_im_scores.R		plot_im_scores.R
score_distribution.py		score_distribution.py

snehitp/patient-similarity

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Patient phenotype and genotype similarity

Usage example

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