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    100 repositories

    • PubMind

      Public
      PubMind is a large language model (LLM)-assisted framework for Publication Mutation and information Discovery, designed to extract variant–disease–pathogenicity…
      Jupyter Notebook
      •
      Other
      •1•4•0•0•Updated Apr 24, 2026Apr 24, 2026

    • PipeVar

      Public
      Pipeline to call phenotype variant
      Nextflow
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • ContextSV

      Public
      An alignment-based, generalized structural variant caller for long-read sequencing/mapping data
      C++
      •
      MIT License
      •0•2•5•0•Updated Apr 21, 2026Apr 21, 2026

    • SCOTCH

      Public
      Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing
      Python
      •
      MIT License
      •3•19•4•0•Updated Apr 16, 2026Apr 16, 2026

    • PhenoGPT2

      Public
      PhenoGPT2 is an advanced phenotype recognition model, leveraging the robust capabilities of large language models.
      Python
      •
      MIT License
      •1•6•1•0•Updated Apr 9, 2026Apr 9, 2026

    • MultiSHAP

      Public
      Python
      •
      MIT License
      •0•7•0•0•Updated Apr 8, 2026Apr 8, 2026

    • REPAIR

      Public
      REPAIR: Reranking via Pairwise Residual Correction for Long-Tailed Classification
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 3, 2026Apr 3, 2026

    • novamod

      Public
      ML project for de novo anomaly-detection-based modification discovery
      Jupyter Notebook
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • CellPathway

      Public
      Cell-type-specific pathway analysis for noncoding de novo variants
      Jupyter Notebook
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • PhenoSnap

      Public
      Rapid extraction of phenotypes and medical entities into Phenopackets from natural texts
      Python
      •0•1•0•0•Updated Mar 26, 2026Mar 26, 2026

    • PhenoSS

      Public
      Phenotype semantic similarity-based approach for rare disease prediction and patient clustering
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Mar 5, 2026Mar 5, 2026

    • RareDAI

      Public
      RareDAI is an advanced LLM technique, fine-tuned on LLama 3.1 models, designed to support genetic counselors and patients in choosing the most appropriate molec…
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • GenoSnap

      Public
      Fast and useful helper scripts for analysis of genotype data in VCF file
      Python
      •0•1•0•0•Updated Feb 26, 2026Feb 26, 2026

    • CoT-RAG-LLM-Gene-Prioritization-Disease-Diagnosis

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated Feb 23, 2026Feb 23, 2026

    • MINT-LLM

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 23, 2026Feb 23, 2026

    • phenoskill

      Public
      An openclaw SKILL for phenotype and medication extraction from chat
      MIT License
      •1•0•0•0•Updated Feb 21, 2026Feb 21, 2026

    • PhenCards

      Public
      Development of phencards.org web server for one stop shop of phenotype information
      HTML
      •1•4•11•1•Updated Feb 20, 2026Feb 20, 2026

    • NanoRepeat

      Public
      NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
      bioinformaticsgenomicssequencing
      bioinformaticsgenomicssequencinggenome-analysisnanopore-sequencingshort-tandem-repeatspacbio-sequencingrepeat-detection
      Python
      •
      MIT License
      •4•19•6•0•Updated Jan 13, 2026Jan 13, 2026

    • PDIDB-webapp

      Public
      Webpage for Phenotype Disease Image Database
      HTML
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • Multimodal-Variant-Effect-Model

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Dec 5, 2025Dec 5, 2025

    • PDIDB

      Public
      Phenotype Diseased Image Synthesis Database
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 3, 2025Dec 3, 2025

    • LongReadSum

      Public
      C++
      •
      MIT License
      •3•29•5•0•Updated Sep 11, 2025Sep 11, 2025

    • RankVar

      Public
      Python
      •0•4•0•0•Updated Aug 26, 2025Aug 26, 2025

    • doc-ANNOVAR

      Public
      Documentation for the ANNOVAR software
      434•250•135•0•Updated Jul 30, 2025Jul 30, 2025

    • QuantitativeGenomics2025

      Public
      Materials for Quantitative Genomics 2025 workshop
      MIT License
      •3•3•0•0•Updated Jul 7, 2025Jul 7, 2025

    • mutformer

      Public
      A transformer model to predict pathogenic mutations
      Jupyter Notebook
      •
      Apache License 2.0
      •2•12•1•0•Updated Jun 25, 2025Jun 25, 2025

    • Gene-Fusion-Detection-Pipeline-LRS

      Public
      The Gene Fusion (GF) Detection Pipeline is comprehensive bioinformatics workflow designed for Oxford Nanopore long-read sequencing data.
      Jupyter Notebook
      •0•3•0•0•Updated Jun 11, 2025Jun 11, 2025

    • SPARK_de_novo_analysis_pipeline

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 28, 2025May 28, 2025

    • LIQA2

      Public
      Python
      •0•0•2•0•Updated Apr 8, 2025Apr 8, 2025

    • LIQA

      Public
      Long-read Isoform Quantification and Analysis
      Python
      •
      Other
      •13•39•0•0•Updated Mar 25, 2025Mar 25, 2025
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