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    79 repositories

    • ContextSV

      Public
      An alignment-based, generalized structural variant caller for long-read sequencing/mapping data
      C++
      •
      MIT License
      •0•2•5•0•Updated Oct 25, 2024Oct 25, 2024

    • doc-ANNOVAR

      Public
      Documentation for the ANNOVAR software
      353•232•122•0•Updated Oct 24, 2024Oct 24, 2024

    • 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•1•2•0•Updated Oct 22, 2024Oct 22, 2024

    • LongReadSum

      Public
      C++
      •
      MIT License
      •2•13•5•0•Updated Sep 27, 2024Sep 27, 2024

    • PhenoGPT

      Public
      Jupyter Notebook
      •
      MIT License
      •5•17•4•0•Updated Sep 20, 2024Sep 20, 2024

    • phenopacket2prompt

      Public
      GA4GH Phenopacket to LLM prompt
      Java
      •
      MIT License
      •1•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
      •0•1•0•0•Updated Aug 12, 2024Aug 12, 2024

    • DeepMod2

      Public
      DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
      deep-learningmethylationnanopore-sequencing
      Jupyter Notebook
      •
      MIT License
      •2•33•11•0•Updated Aug 9, 2024Aug 9, 2024

    • LIQA

      Public
      Long-read Isoform Quantification and Analysis
      Python
      •
      Other
      •13•39•1•0•Updated Aug 8, 2024Aug 8, 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•1•0•0•Updated Jul 17, 2024Jul 17, 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•15•3•0•Updated Jul 17, 2024Jul 17, 2024

    • Project_Belka

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

    • PhenoSS

      Public
      MIT License
      •0•0•0•0•Updated Jul 1, 2024Jul 1, 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•0•0•0•Updated May 28, 2024May 28, 2024

    • PennCNV

      Public
      Copy number vaiation detection from SNP arrays
      C
      •
      Other
      •53•89•56•0•Updated May 19, 2024May 19, 2024

    • NanoCaller

      Public
      Variant calling tool for long-read sequencing data
      Python
      •
      MIT License
      •8•100•28•0•Updated May 14, 2024May 14, 2024

    • PhenoSV

      Public
      PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
      transformerphenotypingstructural-variantsvariant-interpretation
      Python
      •
      MIT License
      •3•16•1•0•Updated Apr 19, 2024Apr 19, 2024

    • biocluster

      Public
      Tutorial on building a computing cluster for bioinformatics
      37•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

    • mutformer

      Public
      A transformer model to predict pathogenic mutations
      Jupyter Notebook
      •
      Apache License 2.0
      •2•11•1•0•Updated Aug 7, 2023Aug 7, 2023

    • LinkedSV

      Public
      C
      •
      MIT License
      •8•21•14•0•Updated Aug 1, 2023Aug 1, 2023

    • EHR-Phenolyzer

      Public
      A pipeline that takes clinical notes from EHRs and generate phenotype terms, then generate ranked gene list
      Python
      •12•36•1•2•Updated Jul 25, 2023Jul 25, 2023

    • QuantitativeGenomics2023

      Public
      Materials for Quantitative Genomics 2023 workshop
      MIT License
      •2•2•0•0•Updated Jun 14, 2023Jun 14, 2023