Skip to content

@collaborativebioinformatics collaborativebioinformatics

Change the repository type filter

All

    Repositories list

    134 repositories

    • NIMR

      Public
      A set of jupyter notebooks to run NVIDIA BioNeMo NIMs, and tune BioNeMo Open Models with R
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • GPU2_Genomic_Cluster_Engine

      Public
      GPU based pipeline for establishing genomic background in European and international biobanks
      Python
      •
      MIT License
      •4•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • Genomic_Cluster_Engine

      Public
      Elixir BioHackathon 2025 Project 4: Beyond beacons: Establishing genomic background in European and international biobanks
      Python
      •
      MIT License
      •4•6•0•0•Updated Jul 13, 2026Jul 13, 2026

    • GPUnative_Genomic_Cluster_Engine

      Public archive
      Establishing genomic background in large genomic datasets
      Python
      •
      MIT License
      •4•0•0•0•Updated Jul 6, 2026Jul 6, 2026

    • MoVana

      Public
      MOsaic structural Variants ANnonation in cAncer
      WDL
      •
      MIT License
      •0•1•0•0•Updated Jul 2, 2026Jul 2, 2026

    • Blended_seq_imputation

      Public
      a Nextflow pipeline for generating imputation reference panels using 1000 Genomes and HGDP data to enhance variant calling in Blended Genome Exome sequencing
      dockerbioinformaticsnextflow
      dockerbioinformaticsnextflowglimpsebcftools1000genomesblended-genome-exome
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jun 27, 2026Jun 27, 2026

    • MethSmoothEval

      Public
      Jupyter Notebook
      •
      MIT License
      •1•6•0•0•Updated May 30, 2026May 30, 2026

    • Network_modeling_multimodal_v003

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • Network_modeling_vNF_002

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • OncoLearn

      Public
      Cancer Biomarker Discovery
      Jupyter Notebook
      •
      MIT License
      •6•7•8•0•Updated Mar 15, 2026Mar 15, 2026

    • RAIDers

      Public
      RAIDers
      Jupyter Notebook
      •
      MIT License
      •2•5•0•0•Updated Mar 13, 2026Mar 13, 2026

    • Network_modeling_v002

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • FedGen

      Public
      Federated Learning (FL) Infrastructure & Synthetic Data
      Python
      •
      MIT License
      •3•7•5•1•Updated Jan 23, 2026Jan 23, 2026

    • omnigenome

      Public
      Pangenome & Genomic Cluster Modeling
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated Jan 13, 2026Jan 13, 2026

    • FedViz

      Public
      Visual Analytics for Cross-Site Biomedical Data and Federated Model Evaluation
      TypeScript
      •
      MIT License
      •0•2•0•0•Updated Jan 10, 2026Jan 10, 2026

    • MuFFLe

      Public
      Knowledge structures for Multimodal Models
      Jupyter Notebook
      •
      MIT License
      •6•4•0•0•Updated Jan 9, 2026Jan 9, 2026

    • PRSAggretator

      Public
      Polygenic Risk Aggregation in common diseases and phenotypes
      Python
      •
      MIT License
      •1•2•0•0•Updated Jan 9, 2026Jan 9, 2026

    • FedPathHarmony

      Public
      FedPathHarmony: Federated Harmonization for Multi-Center Digital Pathology
      harmonizationdigital-pathologyfederated-learning
      harmonizationdigital-pathologyfederated-learningnvflare
      Python
      •
      MIT License
      •4•1•0•0•Updated Jan 9, 2026Jan 9, 2026

    • Med_SNP_Deconvolution

      Public
      Deconvolution of medically relevant SNPs
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • FedProFit

      Public
      Protein modeling for combinatorial mutations
      Python
      •
      MIT License
      •1•1•0•0•Updated Jan 9, 2026Jan 9, 2026

    • HaploblocksBH25_manuscript

      Public
      TeX
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • IsoSV

      Public
      Python
      •3•4•0•0•Updated Dec 2, 2025Dec 2, 2025

    • ODP_hackathon_supplemental_materials

      Public
      Supplemental Materials from the AWS ODP - NVIDIA Knowledge Graph Hackathon
      MIT License
      •0•1•0•0•Updated Dec 1, 2025Dec 1, 2025

    • GeNETwork

      Public
      Build a knowledge graph connecting variants, drugs, and clinical evidence to identify therapeutic opportunities (e.g. CIViC - Clinical Interpretations of Varian…
      Python
      •
      MIT License
      •0•2•0•1•Updated Nov 4, 2025Nov 4, 2025

    • BioGraphRAG

      Public
      Implement a system to use GNN and/or LLM to use knowledge graphs to integrate literature with knowledge graphs made from large public datasets (CIVIC, TCGA, CPT…
      Python
      •
      MIT License
      •3•10•0•0•Updated Oct 10, 2025Oct 10, 2025

    • ClassiGraph

      Public
      Develop a graph neural network to integrate proteomic and genomic features for cancer subtype classification (e.g. CPTAC-2 and CPTAC-3 breast, colorectal, and o…
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Oct 9, 2025Oct 9, 2025

    • EasyGiraffe

      Public
      Simulating and validating multi-centric variant extraction with VG Giraffe.
      Python
      •
      MIT License
      •0•3•0•0•Updated Oct 6, 2025Oct 6, 2025

    • CNVision

      Public
      Python
      •
      MIT License
      •2•8•0•0•Updated Oct 5, 2025Oct 5, 2025

    • Model_Garbage_Collection

      Public
      Implement a system to prune erroneous model assertions in knowledge graphs derived from GNN and/or LLM models or agents.
      Python
      •
      MIT License
      •1•8•0•0•Updated Oct 5, 2025Oct 5, 2025

    • MIDAS

      Public
      Implement a system to combine existing knowledge graphs (e.g. DisGeNet) with primary datasets (e.g. TCGA, 1000 genomes)
      Python
      •
      MIT License
      •1•3•0•0•Updated Oct 3, 2025Oct 3, 2025
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.