Repositories list

• Genomic_context

  Public
  Protein function prediction in bacteria using genomic context

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Feb 13, 2025Feb 13, 2025

• pangenome

  Public
  Pangenome workflow in CWL

  Common Workflow Language

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Feb 2, 2025Feb 2, 2025

• PU-GO

  Public
  Predicting protein functions using positive-unlabeled ranking with ontology-based priors

  protein-function-predictionpositive-unlabeled-learning

  Python

  •2•3•1•0•Updated Jan 29, 2025Jan 29, 2025

• mowl

  Public
  mOWL: Machine Learning library with Ontologies

  machine-learningontologiesneural-symbolic+ 2neuro-symbolicneurosymbolic

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5•63•6•2•Updated Jan 27, 2025Jan 27, 2025

• catE

  Public
  Lattice-preserving ALC ontology embeddings

  category-theoryneuro-symbolic-aiontology-embedding+ 1approximate-reasoning

  Python

  •2•1•0•0•Updated Jan 5, 2025Jan 5, 2025

• EnzBuilder

  Public
  An iterative ML-based metabolic reconstruction framework; Simultaneously Improving Metabolic Model Reconstruction and Enzyme Function Annotation

  Python

  •1•0•0•0•Updated Dec 30, 2024Dec 30, 2024

• DELE

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 30, 2024Nov 30, 2024

• mrsa-sequences

  Public
  Arvados sequence uploader and analyzer for MRSA project

  Python

  •1•0•2•8•Updated Nov 27, 2024Nov 27, 2024

• deepgometa

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•6•0•0•Updated Nov 19, 2024Nov 19, 2024

• Causal-relations-between-diseases

  Public
  0•1•0•0•Updated Oct 2, 2024Oct 2, 2024

• jcel

  Public
  Reasoner for the description logic EL+.

  Java

  •

  Apache License 2.0

  •6•1•0•0•Updated Sep 28, 2024Sep 28, 2024

• hguploader

  Public
  Common Workflow Language

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• FunEq

  Public
  Lean

  •

  Creative Commons Zero v1.0 Universal

  •0•2•0•0•Updated Sep 17, 2024Sep 17, 2024

• deepgo2

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4•35•7•0•Updated Sep 11, 2024Sep 11, 2024

• reasoning-augmented-generation

  Public
  Reasoning Augmented Generation - BH 2024

  Python

  •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

• STARVar

  Public
  STARVar:Symptom based Tool for Automatic Ranking of Variants using evidence from literature and genomes

  text-mininggenomics-datavariant-priorisation+ 1variant-ranking

  Python

  •1•5•0•1•Updated Jul 30, 2024Jul 30, 2024

• gda_analysis

  Public
  Python

  •1•0•0•0•Updated Jul 24, 2024Jul 24, 2024

• FEAS

  Public
  Python

  •0•0•0•0•Updated Jul 9, 2024Jul 9, 2024

• predCAN

  Public
  Ontology-based prediction of cancer driver genes

  machine-learningdriver-genesontology+ 1embeddings

  Python

  •

  BSD 2-Clause "Simplified" License

  •4•5•0•2•Updated Jun 17, 2024Jun 17, 2024

• pathophenodb

  Public
  Web application and additional content for PathoPhenoDB

  Python

  •0•8•2•5•Updated Jun 9, 2024Jun 9, 2024

• KSA001

  Public
  Telomere-2-Telomere Genome from Saudi Arabia

  genome-assemblyreference-genomepersonal-genomics

  Common Workflow Language

  •

  Other

  •0•3•0•0•Updated Jun 2, 2024Jun 2, 2024

• 16SProcessing

  Public
  A Nextflow workflow to run vsearch for short read 16S data

  Nextflow

  •0•1•0•0•Updated May 29, 2024May 29, 2024

• geometric_embeddings

  Public
  Python

  •0•0•0•0•Updated May 15, 2024May 15, 2024

• deepgoweb

  Public
  webappgene-ontology

  JavaScript

  •1•1•0•12•Updated Apr 23, 2024Apr 23, 2024

• deepgoplus

  Public
  DeepGO with GOPlus axioms

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •41•90•18•2•Updated Apr 23, 2024Apr 23, 2024

• EmbedPVP

  Public
  EmbedPVP: Embedding-based Phenotype Variant Predictor

  bioinformaticsvariant-analysisneuro-symbolic+ 4biomedical-ontologiesprioritization-algorithmgenomic-variantsknowledge-enhanced-learning

  Python

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Apr 4, 2024Apr 4, 2024

• LLM_GenePrioritization

  Public
  Python

  •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

• semrec2023

  Public
  Python

  •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• Metagenomic-DeepFRI

  Public
  Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•0•0•0•Updated Mar 13, 2024Mar 13, 2024

• foldcomp

  Public
  Compressing protein structures effectively with torsion angles

  C++

  •

  GNU General Public License v3.0

  •14•0•0•0•Updated Feb 6, 2024Feb 6, 2024