phenotypes | Topic | Ecosyste.ms: Repos

Topic: "phenotypes"

exomiser/Exomiser

A Tool to Annotate and Prioritize Exome Variants

Language: Java - Size: 280 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 210 - Forks: 53

ClarityNLP/ClarityNLP 📦

An NLP framework for clinical phenotyping. Docker | Python | Solr | OMOP. http://claritynlp.readthedocs.io/en/latest/

Language: Jupyter Notebook - Size: 190 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 105 - Forks: 42

phenopackets/phenopacket-schema

Repository for the GA4GH phenopacket schema

Language: Java - Size: 1.45 MB - Last synced at: 20 days ago - Pushed at: 9 months ago - Stars: 86 - Forks: 31

GeneDx/phenopy

Phenotype comparison tools using semantic similarity.

Language: Python - Size: 17.9 MB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 64 - Forks: 10

monarch-initiative/biolink-api

API for linked biological knowledge

Language: Python - Size: 1.19 MB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 64 - Forks: 25

pato-ontology/pato

PATO - the Phenotype And Trait Ontology

Language: Makefile - Size: 46.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 59 - Forks: 18

aldro61/kover

Learn interpretable computational phenotyping models from k-merized genomic data

Language: Python - Size: 4.38 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 50 - Forks: 16

bio-ontology-research-group/phenomenet-vp

A phenotype-based tool for variant prioritization in WES and WGS data

Language: Java - Size: 6.53 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 34 - Forks: 13

ArcInstitute/ScreenPro2

Flexible analysis of high-content CRISPR screening

Language: Python - Size: 3.53 MB - Last synced at: 8 days ago - Pushed at: about 2 months ago - Stars: 31 - Forks: 6

GeneDx/txt2hpo

Python library for extracting HPO encoded phenotypes from text

Language: Python - Size: 44.7 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 29 - Forks: 4

obophenotype/bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)

Language: Jupyter Notebook - Size: 273 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 27 - Forks: 11

mims-harvard/ProCyon

ProCyon: A multimodal foundation model for protein phenotypes

Language: Python - Size: 11.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 7

MRCIEU/epigraphdb-r

R package for epigraphdb

Language: R - Size: 5.88 MB - Last synced at: 12 days ago - Pushed at: 11 months ago - Stars: 27 - Forks: 8

monarch-initiative/phenol

phenol: Phenotype ontology library

Language: Java - Size: 18.5 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 23 - Forks: 4

drseb/HPO-translations

Internationalisation of the HPO content

Size: 11.6 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 19 - Forks: 12

Knowledge-Graph-Hub/kg-microbe

Language: Jupyter Notebook - Size: 529 MB - Last synced at: 16 days ago - Pushed at: 27 days ago - Stars: 18 - Forks: 3

germinateplatform/germinate-vue

Germinate is an open source plant database infrastructure and application programming platform on which complex data from genetic resource collections can be stored, queried and visualized.

Language: Vue - Size: 10.6 MB - Last synced at: 3 days ago - Pushed at: 21 days ago - Stars: 17 - Forks: 4

pombase/fypo

Fission Yeast Phenotype Ontology

Language: Makefile - Size: 964 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 16 - Forks: 6

RomanoLab/comptox_ai

ComptoxAI - An artificial Intelligence toolkit for computational toxicology

Language: Python - Size: 12.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 5

open-traits-network/open-traits-network.github.io

Open Traits Network Registry and Website

Language: CSS - Size: 156 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 13 - Forks: 58

monarch-initiative/phenogrid

The phenogrid widget

Language: JavaScript - Size: 23 MB - Last synced at: 4 days ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 14

PheMA/cql-on-omop

Runs CQL phenotype definitions against an OMOP repository

Language: Java - Size: 2.14 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 12 - Forks: 2

sigven/phenOncoX

Crossmapped phenotype ontologies for the oncology domain

Language: R - Size: 554 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 0

ncbi/DbGaP-FHIR-API-Docs

The documentation repository for the dbGaP FHIR API.

Language: Jupyter Notebook - Size: 11.6 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 11 - Forks: 3

obophenotype/c-elegans-phenotype-ontology

Ontology for phenotypes pertaining to the nematode Caenorhabditis elegans and related nematodes used by the nematode genome database WormBase

Language: Makefile - Size: 107 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 11 - Forks: 4

lasigeBioTM/PGR

A Silver Standard Corpus of Human Phenotype-Gene Relations

Language: Python - Size: 4.98 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 3

intervene-EU-H2020/synthetic_data

Software program for generating synthetic datasets for genotypes and phenotypes

Language: Jupyter Notebook - Size: 82.2 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 2

This is a set of useful tools for using, creating, validating and generally working with Codelists in Health Research. The tools are in Rust with Python and R bindings so they can be used in any of the 3 languages.

Language: Rust - Size: 229 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 8 - Forks: 2

cmungall/linkml-phenopackets

EXPERIMENTAL rendering of phenopackets in linkml

Language: Python - Size: 11.4 MB - Last synced at: 28 days ago - Pushed at: 11 months ago - Stars: 8 - Forks: 0

chopdgd/django-phenotype-ontologies

Django app for parsing/loading Phenotype ontologies (HPO, MONDO, OncoTree, etc)

Language: Python - Size: 262 KB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 7 - Forks: 1

xperthut/HYPPO-X

Algebraic topology based header only library to extract insight of complex high dimensional data.

Language: HTML - Size: 26.6 MB - Last synced at: 10 months ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 3

drseb/HPO-archive

HPO archive of the ontology and annotations

Size: 1.12 GB - Last synced at: about 2 months ago - Pushed at: about 8 years ago - Stars: 7 - Forks: 2

nathadriele/biophenotype-rag

This project implements a RAG (Retrieval-Augmented Generation) application to answer questions about phenotypes using biological and genomic data. The pipeline integrates information retrieval with response generation via language models (LLM), facilitating accurate analysis of phenotypic data.

Language: Jupyter Notebook - Size: 584 KB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 0

obophenotype/dicty-phenotype-ontology

Dicty Phenotype Ontology

Language: Makefile - Size: 2.89 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 3

obophenotype/planarian-phenotype-ontology

Planarian Phenotype Ontology

Language: Makefile - Size: 11.9 MB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

phenopackets/phenopacket-reference-implementation 📦

Reference java implementation for phenopackets

Language: Java - Size: 677 KB - Last synced at: 12 months ago - Pushed at: over 6 years ago - Stars: 6 - Forks: 9

andreariba/PheLiM

Estimation of gene contributions to the phenotype from genome-wide RNA interfence experiment.

Language: Perl - Size: 2.14 MB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 6 - Forks: 1

drseb/boqa

Bayesian ontology querying from Bauer et al.

Language: Java - Size: 202 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 6

germinateplatform/germinate 📦

Germinate is an open source plant database infrastructure and application programming platform on which complex data from genetic resource collections can be stored, queried and visualized using common, reusable programming components.

Language: Java - Size: 197 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 1

zietzm/phenotype_standardization

https://github.com/zietzm/phenotype_standardization/wiki

Language: Python - Size: 57.6 KB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 0

monarch-initiative/monarch-phenote 📦

stub for monarch phenote

Language: Java - Size: 138 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 4 - Forks: 3

Phenomics/phenomics.github.io

Website for the Phenomics and Machine Learning Team

Language: HTML - Size: 2.97 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 5

bio2bel/mesh

A Bio2BEL package for the Medical Subject Headings (MeSH; https://meshb.nlm.nih.gov)

Language: Python - Size: 74.2 KB - Last synced at: 24 days ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

drseb/phenopposites

Project to generate phenotype opposite_of relationships and investigate the effect on ontology-based algorithms

Size: 19.5 KB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 2

SNP2Pheno/SNP2Pheno

Study Project MBI 2025

Language: QML - Size: 81.1 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 2 - Forks: 0

monarch-initiative/phenotype2phenopacket

Phenotype2Phenopacket is a command-line tool that converts a phenotype annotation into GA4GH Phenopackets, facilitating standardised phenotypic data representation.

Language: Python - Size: 4.29 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 2

UofS-Pulse-Binfo/rawphenotypes

A Tripal module for storing raw phenotypic data. Specifically meant to help researchers contribute raw data, visualize summaries and download for further analysis.

Language: PHP - Size: 1.73 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 2

drseb/annotation-simulation

Code to generate ontology annotated objects (e.g. HPO annotated patients)

Language: Java - Size: 3.14 MB - Last synced at: about 2 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 1

obophenotype/zebrafish-phenotype-ontology-build

:fish: Zebrafish Phenotype Ontology: Build Tools (OBSOLETE)

Language: Java - Size: 32.8 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 1

julianflowers/myScrapers

Functions to extract web data from PHE sites

Language: HTML - Size: 32.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 1

tatonetti-lab/indirect-gwas-analysis

Accerating pan-biobank GWAS using phenotype projections

Language: Jupyter Notebook - Size: 5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

k-yumin/punnett-square

making punnett square on excel and calculating the phenotypic ratio.

Language: Jupyter Notebook - Size: 21.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

jillagal/deathToy

How do proliferation-migration tradeoffs affect phenotypic evolution in a tumors? In this off-lattice agent-based simulation the user can vary trade-off boundaries, death rate, and whether death occurs in response to demographic or environmental stochasticity. See the README file for details.

Language: Java - Size: 217 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

bio2bel/mir2disease

A Bio2BEL package for mir2disease (http://www.mir2disease.org)

Language: Python - Size: 28.3 KB - Last synced at: 7 months ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

drseb/hpoweb

HPO web browser created with Vaadin

Language: CSS - Size: 1.02 MB - Last synced at: about 2 months ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

drseb/hpo-owl-qc

The QC software for the OWL version of HPO (only text-checks, not so much logic included)

Language: Java - Size: 51.8 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 1

yenon118/SoybeanGenVarX

The Soybean Genomic Variations Explorer (Soybean GenVarX) is a toolset that consists of promoter region component and CNV component for users to perform queries, visualize data, and conduct annotations using genotypic and phenotypic differences.

Language: PHP - Size: 9.79 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

YADengUU/censGWAS

Perform GWAS on Phenotype Measurements Subject to Limit of Detection for Biobank-Scale Dataset

Language: R - Size: 312 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

comorbidity/medgen-umls

NCBI Medical Genetics, UMLS Unified Medical Language System Concepts and PubMed linked citations

Language: Shell - Size: 5.17 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

yenon118/GenVarX

The Genomic Variations Explorer (GenVarX) is a toolset that consists of promoter region component and CNV component for users to perform queries, visualize data, and conduct annotations using genotypic and phenotypic differences.

Language: JavaScript - Size: 24.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

UofS-Pulse-Binfo/analyzedphenotypes

Tripal/Drupal support for analyzed phenotypic data including data loaders, exporters, trait pages and summaries on germplasm pages.

Language: PHP - Size: 10.9 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

ClarityNLP/results-viewer

A user interface for exploring and evaluating results from the ClarityNLP clinical phenotype application.

Language: JavaScript - Size: 6.43 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

yenon118/MViz 📦

MViz: A Toolset for Annotating Promoter and CNV Regions Using Genotypic and Phenotypic Differences

Language: JavaScript - Size: 20.6 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0