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    117 repositories

    • Haploblock_Clusters_ElixirBH25

      Public
      Elixir BioHackathon 2025 Project 4: Beyond beacons: Establishing genomic background in European and international biobanks
      Python
      •
      MIT License
      •2•4•0•0•Updated Nov 7, 2025Nov 7, 2025

    • GeNETwork

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

    • ODP_hackathon_supplemental_materials

      Public
      Supplemental Materials from the AWS ODP - NVIDIA Knowledge Graph Hackathon
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 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, CPTAC)
      Python
      •
      MIT License
      •1•2•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 ovarian cancer data)
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • EasyGiraffe

      Public
      Simulating and validating multi-centric variant extraction with VG Giraffe.
      Python
      •
      MIT License
      •0•1•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•5•0•0•Updated Oct 5, 2025Oct 5, 2025

    • MethSmoothEval

      Public
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Oct 4, 2025Oct 4, 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•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • ECoGraph

      Public
      Build a knowledge graph integrating cancer genomics data to identify potential biomarkers and therapeutic targets (e.g. TCGA)
      Jupyter Notebook
      •
      MIT License
      •2•3•1•0•Updated Oct 3, 2025Oct 3, 2025

    • Human_Haploblock_Lengths

      Public
      Python
      •
      MIT License
      •1•2•0•0•Updated Oct 1, 2025Oct 1, 2025

    • Microbe_KG

      Public
      Develop a knowledge graph linking microbiome compositions to various diseases and health conditions (e.g. Human Microbiome Project HMP)
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • Brain_connect_KG

      Public
      Develop a knowledge graph linking brain connectivity data with neurological disorders to identify potential biomarkers (e.g. Human Connectome Project)
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • IsoSV

      Public
      Python
      •3•3•0•0•Updated Sep 27, 2025Sep 27, 2025

    • Mosaicome

      Public
      Shell
      •
      MIT License
      •3•13•0•0•Updated Sep 18, 2025Sep 18, 2025

    • MoVana

      Public
      WDL
      •
      MIT License
      •0•1•0•0•Updated Sep 10, 2025Sep 10, 2025

    • Proteolinker

      Public
      R
      •
      MIT License
      •2•1•0•0•Updated Aug 30, 2025Aug 30, 2025

    • TRACE

      Public
      Transposable element Recognition And Comprehensive Evaluation
      Python
      •
      MIT License
      •4•3•0•0•Updated Aug 30, 2025Aug 30, 2025

    • MetaTango

      Public
      MetaTango is a benchmarking pipeline for evaluating structural variant (SV) calling in microbiome datasets. It provides a direct comparison between reference-based methods (e.g., Sniffles2) and graph-based methods (e.g., Rhea)
      Python
      •
      MIT License
      •1•1•0•1•Updated Aug 29, 2025Aug 29, 2025

    • Phenome-Mapper

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • GPU_MSA_Integration

      Public
      MIT License
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • BioAI_manuscript

      Public
      TeX
      •
      MIT License
      •0•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • Haplotype_matrix_clustering

      Public
      matrixhaplotypespcadnanexus1000genomeshaplotypeplink2haplotype-clusteringarg-needlebiohackathon-cmu-2025
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 2, 2025May 2, 2025

    • Cis_and_trans_effects_on_variant_penetrance

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

    • 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
      dockerbioinformaticsnextflowglimpsebcftools1000genomesblended-genome-exome
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Mar 10, 2025Mar 10, 2025

    • Multiomic_graph

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 7, 2025Mar 7, 2025

    • Longitudinal_emr_accleRation

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 5, 2025Mar 5, 2025

    • LenskAI

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Mar 5, 2025Mar 5, 2025

    • LLM_SVs

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024