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    • 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
      1400Updated Apr 24, 2026Apr 24, 2026
    • PipeVar

      Public
      Pipeline to call phenotype variant
      Nextflow
      0000Updated Apr 23, 2026Apr 23, 2026
    • ContextSV

      Public
      An alignment-based, generalized structural variant caller for long-read sequencing/mapping data
      C++
      MIT License
      0250Updated 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
      31940Updated 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
      1610Updated Apr 9, 2026Apr 9, 2026
    • MultiSHAP

      Public
      Python
      MIT License
      0700Updated Apr 8, 2026Apr 8, 2026
    • REPAIR

      Public
      REPAIR: Reranking via Pairwise Residual Correction for Long-Tailed Classification
      Python
      MIT License
      0200Updated Apr 3, 2026Apr 3, 2026
    • novamod

      Public
      ML project for de novo anomaly-detection-based modification discovery
      Jupyter Notebook
      0000Updated Apr 1, 2026Apr 1, 2026
    • Cell-type-specific pathway analysis for noncoding de novo variants
      Jupyter Notebook
      0000Updated Mar 30, 2026Mar 30, 2026
    • PhenoSnap

      Public
      Rapid extraction of phenotypes and medical entities into Phenopackets from natural texts
      Python
      0100Updated Mar 26, 2026Mar 26, 2026
    • PhenoSS

      Public
      Phenotype semantic similarity-based approach for rare disease prediction and patient clustering
      Jupyter Notebook
      MIT License
      0200Updated 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
      0000Updated Mar 5, 2026Mar 5, 2026
    • GenoSnap

      Public
      Fast and useful helper scripts for analysis of genotype data in VCF file
      Python
      0100Updated Feb 26, 2026Feb 26, 2026
    • Python
      MIT License
      0400Updated Feb 23, 2026Feb 23, 2026
    • MINT-LLM

      Public
      Python
      MIT License
      0100Updated Feb 23, 2026Feb 23, 2026
    • An openclaw SKILL for phenotype and medication extraction from chat
      MIT License
      1000Updated Feb 21, 2026Feb 21, 2026
    • PhenCards

      Public
      Development of phencards.org web server for one stop shop of phenotype information
      HTML
      14111Updated Feb 20, 2026Feb 20, 2026
    • NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
      Python
      MIT License
      41960Updated Jan 13, 2026Jan 13, 2026
    • Webpage for Phenotype Disease Image Database
      HTML
      0000Updated Dec 16, 2025Dec 16, 2025
    • Jupyter Notebook
      0010Updated Dec 5, 2025Dec 5, 2025
    • PDIDB

      Public
      Phenotype Diseased Image Synthesis Database
      Python
      MIT License
      0100Updated Dec 3, 2025Dec 3, 2025
    • C++
      MIT License
      32950Updated Sep 11, 2025Sep 11, 2025
    • RankVar

      Public
      Python
      0400Updated Aug 26, 2025Aug 26, 2025
    • Documentation for the ANNOVAR software
      4342501350Updated Jul 30, 2025Jul 30, 2025
    • Materials for Quantitative Genomics 2025 workshop
      MIT License
      3300Updated Jul 7, 2025Jul 7, 2025
    • mutformer

      Public
      A transformer model to predict pathogenic mutations
      Jupyter Notebook
      Apache License 2.0
      21210Updated Jun 25, 2025Jun 25, 2025
    • The Gene Fusion (GF) Detection Pipeline is comprehensive bioinformatics workflow designed for Oxford Nanopore long-read sequencing data.
      Jupyter Notebook
      0300Updated Jun 11, 2025Jun 11, 2025
    • Jupyter Notebook
      0000Updated May 28, 2025May 28, 2025
    • LIQA2

      Public
      Python
      0020Updated Apr 8, 2025Apr 8, 2025
    • LIQA

      Public
      Long-read Isoform Quantification and Analysis
      Python
      Other
      133900Updated Mar 25, 2025Mar 25, 2025
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