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    25 repositories

    • ChimeraLM

      Public
      A genomic language model that distinguishes true structural variants from artifacts in long-read whole genome amplification
      bioinformaticsdeep-learninggenomicsbamsingle-cellstructural-variation
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Nov 20, 2025Nov 20, 2025

    • yanglab-guide

      Public
      The repo contain content about yang's lab guide.
      developmentguidelab
      Python
      •
      MIT License
      •2•2•0•0•Updated Nov 18, 2025Nov 18, 2025

    • DeepChopper

      Public
      Language models identify chimeric artificial reads in NanoPore direct-RNA sequencing data.
      bioinformaticsdeep-learningnanoporebiologylong-read-sequencing
      Rust
      •
      Apache License 2.0
      •1•5•0•1•Updated Nov 18, 2025Nov 18, 2025

    • pxblat

      Public
      PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT
      pythoncbioinformaticscppalignmentblatpybind11sequence-analysis
      C
      •
      Other
      •0•17•0•1•Updated Nov 16, 2025Nov 16, 2025

    • ylab-hi.github.io

      Public
      Official website for Yang Lab
      SCSS
      •0•0•0•0•Updated Nov 4, 2025Nov 4, 2025

    • ScanNeo2

      Public
      Snakemake-based computational workflow for neoantigen prediction from diverse sources
      snakemakegene-fusionindelsimmunotherapyvaccinepeptidesnakemake-workflowsplicingepitopeneoantigens
      Python
      •
      MIT License
      •1•14•8•0•Updated Nov 1, 2025Nov 1, 2025

    • nf_hichip

      Public
      A simple nextflow pipeline for HiChIP data processing
      Nextflow
      •0•1•0•0•Updated Oct 30, 2025Oct 30, 2025

    • trans_lncRNA

      Public
      Public repository containing research code for the trans-acting lncRNA project
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 11, 2025Oct 11, 2025

    • EasyEvo2

      Public
      To use Evo2 easily
      Python
      •
      MIT License
      •0•11•1•0•Updated Sep 30, 2025Sep 30, 2025

    • OctopuSV

      Public
      Efficient merging of structural variants from multiple SV callers and samples
      Python
      •
      MIT License
      •1•30•3•12•Updated Sep 25, 2025Sep 25, 2025

    • ScanEPIC_dev

      Public
      Exitron detection in short, long and single-cell RNA datasets--developmental fork
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • ScanEPIC

      Public
      Exitron detection in short, long and single-cell RNA datasets
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • segmeter

      Public
      Framework designed for evaluating the performance of genomic interval query tools
      Python
      •0•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • genogrove

      Public
      C++ Genomic Interval B+ Tree Library
      C++
      •
      GNU General Public License v3.0
      •0•3•1•1•Updated Apr 16, 2025Apr 16, 2025

    • TentacleSV

      Public
      A Snakemake-based structural variant analysis workflow leveraging OctopusV's capabilities.
      Python
      •
      MIT License
      •0•10•0•0•Updated Mar 31, 2025Mar 31, 2025

    • SpliceAI-BED

      Public
      Run SpliceAI on BED files
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 24, 2025Jan 24, 2025

    • ScanITD

      Public
      A python tool to detect internal tandem duplication with robust variant allele frequency estimation
      Python
      •
      MIT License
      •3•12•1•0•Updated Jan 3, 2025Jan 3, 2025

    • ScanExitron

      Public
      A computational workflow for exitron splicing identification
      Shell
      •
      MIT License
      •6•12•1•0•Updated Aug 30, 2024Aug 30, 2024

    • docker-images

      Public
      docker-images
      Dockerfile
      •
      MIT License
      •0•1•0•0•Updated Apr 24, 2024Apr 24, 2024

    • ScanExitronLR

      Public
      A package for the characterization and quantification of exitron splicing events in long-read RNA-seq
      pythonbioinformatics-toollong-read-data
      Python
      •
      MIT License
      •0•6•1•1•Updated Aug 5, 2023Aug 5, 2023

    • BINARY

      Public
      BIoiNformatics Algorithms libRarY aka BINARY
      templatelibrarybioinformaticsalgorithmcpphigh-performanceconceptsvcfrangescpp20-standard
      C++
      •
      Apache License 2.0
      •0•2•2•1•Updated Dec 21, 2022Dec 21, 2022

    • ScanNeo

      Public
      A pipeline for identifying indel derived neoantigens using RNA-Seq data
      Python
      •
      Other
      •7•30•6•0•Updated Aug 29, 2022Aug 29, 2022

    • kent

      Public
      UCSC Genome Browser source tree. Stable branch: "beta".
      C
      •
      Other
      •97•0•0•0•Updated Jun 9, 2022Jun 9, 2022

    • pbsim2

      Public
      PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
      C++
      •
      GNU General Public License v2.0
      •18•0•0•0•Updated Feb 18, 2022Feb 18, 2022

    • lncGSEA

      Public
      An R package to identify lncRNA associated pathway
      R
      •
      MIT License
      •0•0•2•0•Updated Aug 13, 2020Aug 13, 2020