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    91 repositories

    • PubMind

      Public
      PubMind is a large language model (LLM)-assisted framework for Publication Mutation and information Discovery, designed to extract variant–disease–pathogenicity relationships directly from biomedical literature.
      Jupyter Notebook
      •
      Other
      •1•3•0•0•Updated Nov 2, 2025Nov 2, 2025

    • 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
      •2•16•2•0•Updated Oct 19, 2025Oct 19, 2025

    • PipeVar

      Public
      Pipeline to call phenotype variant
      Nextflow
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • ContextSV

      Public
      An alignment-based, generalized structural variant caller for long-read sequencing/mapping data
      C++
      •
      MIT License
      •0•2•5•0•Updated Sep 20, 2025Sep 20, 2025

    • LongReadSum

      Public
      C++
      •
      MIT License
      •3•24•4•0•Updated Sep 11, 2025Sep 11, 2025

    • NanoRepeat

      Public
      NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
      bioinformaticsgenomicssequencinggenome-analysisnanopore-sequencingshort-tandem-repeatspacbio-sequencingrepeat-detection
      Python
      •
      MIT License
      •2•20•6•0•Updated Sep 10, 2025Sep 10, 2025

    • PhenoGPT2

      Public
      PhenoGPT2 is an advanced phenotype recognition model, leveraging the robust capabilities of large language models.
      Python
      •
      MIT License
      •1•5•5•0•Updated Aug 27, 2025Aug 27, 2025

    • 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 molecular genetic tests, such as gene panels or WES/WGS, through clear and comprehensive explanations.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 27, 2025Aug 27, 2025

    • RankVar

      Public
      Python
      •0•3•0•0•Updated Aug 26, 2025Aug 26, 2025

    • MultiSHAP

      Public
      Python
      •0•3•0•0•Updated Aug 1, 2025Aug 1, 2025

    • doc-ANNOVAR

      Public
      Documentation for the ANNOVAR software
      416•246•134•0•Updated Jul 30, 2025Jul 30, 2025

    • PhenCards

      Public
      Development of phencards.org web server for one stop shop of phenotype information
      HTML
      •1•4•11•1•Updated Jul 24, 2025Jul 24, 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•2•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

    • MINT-LLM

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 19, 2025May 19, 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•38•0•0•Updated Mar 25, 2025Mar 25, 2025

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

      Public
      MIT License
      •0•3•0•0•Updated Mar 23, 2025Mar 23, 2025

    • NanoCaller

      Public
      Variant calling tool for long-read sequencing data
      Python
      •
      MIT License
      •8•112•33•0•Updated Mar 19, 2025Mar 19, 2025

    • PhenoGPT

      Public
      Jupyter Notebook
      •
      MIT License
      •8•29•4•0•Updated Mar 15, 2025Mar 15, 2025

    • InFuse

      Public
      Software for detecting gene fusions and exon-skippings from long read sequencing
      Python
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • DeepMod2

      Public
      DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
      deep-learningmethylationnanopore-sequencing
      Jupyter Notebook
      •
      MIT License
      •4•55•15•0•Updated Mar 5, 2025Mar 5, 2025

    • CancerVar

      Public
      Clinical interpretation of somatic mutations in cancer
      Python
      •15•49•21•0•Updated Feb 20, 2025Feb 20, 2025

    • LinkedSV

      Public
      C
      •
      MIT License
      •9•20•15•0•Updated Feb 18, 2025Feb 18, 2025

    • PhenoSV

      Public
      PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
      transformerphenotypingstructural-variantsvariant-interpretation
      Python
      •
      MIT License
      •5•17•4•0•Updated Feb 11, 2025Feb 11, 2025

    • PhenoSS

      Public
      MIT License
      •0•1•0•0•Updated Feb 10, 2025Feb 10, 2025

    • AmpBinner

      Public
      A barcode demultiplexer for Oxford Nanopore long-read amplicon sequencing data
      Python
      •
      MIT License
      •2•10•4•0•Updated Nov 27, 2024Nov 27, 2024

    • LlamaDx

      Public
      LlamaDx is an advanced LLM technique, pretrained on LLama 3.2 models, designed to providing some predictions and medical knowledges for doctors, nurses and patients through clear and comprehensive explanations. It is an AI chatbot where the users can ask question and provide relevant information for disease diagnosis.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 24, 2024Nov 24, 2024