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    86 repositories

    • RankVar

      Public
      Python
      •0•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • LIQA

      Public
      Long-read Isoform Quantification and Analysis
      Python
      •
      Other
      •13•39•0•0•Updated Mar 25, 2025Mar 25, 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•6•2•0•Updated Mar 24, 2025Mar 24, 2025

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

      Public
      MIT License
      •0•2•0•0•Updated Mar 23, 2025Mar 23, 2025

    • ContextSV

      Public
      An alignment-based, generalized structural variant caller for long-read sequencing/mapping data
      C++
      •
      MIT License
      •0•2•5•0•Updated Mar 22, 2025Mar 22, 2025

    • doc-ANNOVAR

      Public
      Documentation for the ANNOVAR software
      380•240•130•0•Updated Mar 21, 2025Mar 21, 2025

    • NanoCaller

      Public
      Variant calling tool for long-read sequencing data
      Python
      •
      MIT License
      •8•106•32•0•Updated Mar 19, 2025Mar 19, 2025

    • PhenoGPT

      Public
      Jupyter Notebook
      •
      MIT License
      •6•21•3•0•Updated Mar 15, 2025Mar 15, 2025

    • LIQA2

      Public
      Python
      •0•0•3•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
      •2•45•13•0•Updated Mar 5, 2025Mar 5, 2025

    • CancerVar

      Public
      Clinical interpretation of somatic mutations in cancer
      Python
      •13•45•20•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
      •4•16•3•0•Updated Feb 11, 2025Feb 11, 2025

    • PhenoSS

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

    • LongReadSum

      Public
      C++
      •
      MIT License
      •3•17•5•0•Updated Feb 5, 2025Feb 5, 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 Jan 29, 2025Jan 29, 2025

    • NanoRepeat

      Public
      NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
      genome-analysisnanopore-sequencingshort-tandem-repeatspacbio-sequencingrepeat-detectionbioinformaticsgenomicssequencing
      Python
      •
      MIT License
      •1•18•4•0•Updated Dec 6, 2024Dec 6, 2024

    • 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

    • PhenoGPT2

      Public
      PhenoGPT2 is an advanced phenotype recognition model, leveraging the robust capabilities of large language models.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • phenopacket2prompt

      Public
      GA4GH Phenopacket to LLM prompt
      Java
      •
      MIT License
      •2•0•0•0•Updated Sep 15, 2024Sep 15, 2024

    • Gene-Fusion-Detection-Pipeline-LRS

      Public
      The Gene Fusion (GF) Detection Pipeline is comprehensive bioinformatics workflow designed for Oxford Nanopore long-read sequencing data.
      Python
      •0•1•0•0•Updated Aug 30, 2024Aug 30, 2024

    • GestaltMML

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•1•0•Updated Aug 12, 2024Aug 12, 2024

    • LINE-Expression-LRS

      Public
      Bioinformatics pipeline for the identification and quantification of active, full-length Long INterspersed Elements (LINEs)
      Shell
      •0•0•1•0•Updated Aug 7, 2024Aug 7, 2024

    • Project_SPARK_de_novo_analysis_pipeline

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 20, 2024Jul 20, 2024

    • QuantitativeGenomics2024

      Public
      Materials for Quantitative Genomics 2024 workshop
      MIT License
      •2•2•0•0•Updated Jul 17, 2024Jul 17, 2024

    • Project_Belka

      Public
      Jupyter Notebook
      •0•2•8•0•Updated Jul 9, 2024Jul 9, 2024

    • Reversal_Curse

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 19, 2024Jun 19, 2024

    • DELongSeq

      Public
      Python
      •0•7•0•0•Updated Jun 2, 2024Jun 2, 2024