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    81 repositories

    • ContextSV

      Public
      An alignment-based, generalized structural variant caller for long-read sequencing/mapping data
      C++
      •
      MIT License
      •0•2•5•0•Updated Feb 8, 2025Feb 8, 2025

    • InFuse

      Public
      Software for detecting gene fusions and exon-skippings from long read sequencing
      Python
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • LongReadSum

      Public
      C++
      •
      MIT License
      •3•14•5•0•Updated Feb 5, 2025Feb 5, 2025

    • PhenoSS

      Public
      MIT License
      •0•1•0•0•Updated Feb 2, 2025Feb 2, 2025

    • NanoCaller

      Public
      Variant calling tool for long-read sequencing data
      Python
      •
      MIT License
      •8•103•32•0•Updated Jan 30, 2025Jan 30, 2025

    • LinkedSV

      Public
      C
      •
      MIT License
      •9•21•15•0•Updated Jan 21, 2025Jan 21, 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
      •0•6•4•0•Updated Jan 17, 2025Jan 17, 2025

    • DeepMod2

      Public
      DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
      deep-learningmethylationnanopore-sequencing
      Jupyter Notebook
      •
      MIT License
      •2•41•13•0•Updated Jan 17, 2025Jan 17, 2025

    • LIQA

      Public
      Long-read Isoform Quantification and Analysis
      Python
      •
      Other
      •13•39•0•0•Updated Jan 7, 2025Jan 7, 2025

    • PhenoGPT

      Public
      Jupyter Notebook
      •
      MIT License
      •6•21•2•0•Updated Dec 13, 2024Dec 13, 2024

    • PhenoSV

      Public
      PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
      transformerphenotypingstructural-variantsvariant-interpretation
      Python
      •
      MIT License
      •4•16•2•0•Updated Dec 12, 2024Dec 12, 2024

    • 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

    • doc-ANNOVAR

      Public
      Documentation for the ANNOVAR software
      373•237•128•0•Updated Oct 24, 2024Oct 24, 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

    • SCOTCH_reproduction

      Public
      Reproduction instruction for SCOTCH manuscript
      R
      •
      MIT License
      •0•1•0•0•Updated May 28, 2024May 28, 2024

    • PennCNV

      Public
      Copy number vaiation detection from SNP arrays
      C
      •
      Other
      •56•89•58•0•Updated May 19, 2024May 19, 2024

    • biocluster

      Public
      Tutorial on building a computing cluster for bioinformatics
      36•86•0•0•Updated Nov 28, 2023Nov 28, 2023

    • PhenCards

      Public
      Development of phencards.org web server for one stop shop of phenotype information
      HTML
      •1•5•11•1•Updated Oct 25, 2023Oct 25, 2023

    • Integer_divsibility

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 8, 2023Sep 8, 2023

    • GenGen

      Public
      A set of software tools to facilitate GWAS analysis
      C
      •
      Other
      •10•20•7•0•Updated Aug 29, 2023Aug 29, 2023