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    • Scripts to analyze read alignment and variant calling from simulated and empirical data based on different human reference genome versions.
      Shell
      0000Updated Apr 16, 2026Apr 16, 2026
    • Jupyter Notebook
      0010Updated Apr 9, 2026Apr 9, 2026
    • A repository containing code to correct T>N mutation bias in NovaSeq 6000 callsets
      Jupyter Notebook
      0000Updated Apr 8, 2026Apr 8, 2026
    • HTML
      2000Updated Apr 6, 2026Apr 6, 2026
    • Analysis software for Nanorate Sequencing (NanoSeq) experiments -- forked over from Sanger Institute
      C++
      GNU Affero General Public License v3.0
      15000Updated Apr 2, 2026Apr 2, 2026
    • xTea

      Public
      Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
      Python
      Other
      24124132Updated Mar 10, 2026Mar 10, 2026
    • This repository has the description of the hg38 genome categorization of easy, difficult, and extreme region.
      0100Updated Feb 25, 2026Feb 25, 2026
    • 0000Updated Feb 3, 2026Feb 3, 2026
    • R
      0000Updated Jan 29, 2026Jan 29, 2026
    • Python
      0000Updated Jan 9, 2026Jan 9, 2026
    • A mosaic detecting software based on phasing and random forest
      Python
      MIT License
      217072Updated Dec 8, 2025Dec 8, 2025
    • Repository to host shared code for the lab
      Shell
      0100Updated Nov 10, 2025Nov 10, 2025
    • EchoSV

      Public
      A novel tool for accurately merging haplotype-based SV calls and comparing SVs across reference genomes
      Python
      MIT License
      0600Updated Oct 9, 2025Oct 9, 2025
    • This repository contains analysis of spatially-resolved somatic mutations datasets.
      HTML
      MIT License
      0100Updated Sep 17, 2025Sep 17, 2025
    • r-scan2

      Public
      R package supporting the SCAN2 pipeline
      R
      4020Updated Aug 26, 2025Aug 26, 2025
    • HiScanner

      Public
      C
      MIT License
      2830Updated Aug 13, 2025Aug 13, 2025
    • bamsnap

      Public
      HTML
      MIT License
      29125200Updated Aug 1, 2025Aug 1, 2025
    • JavaScript
      MIT License
      0000Updated Jul 30, 2025Jul 30, 2025
    • SCAN2

      Public
      SCAN2 is a somatic SNV and indel genotyper for single cells amplified by Primary Template-Directed Amplification (PTA)
      Python
      917171Updated Jul 28, 2025Jul 28, 2025
    • ViScanner

      Public
      Scanner output visualization tool
      JavaScript
      0000Updated Jul 15, 2025Jul 15, 2025
    • Analyze distribution of somatic mutations with permutations as a background
      R
      0000Updated Jul 7, 2025Jul 7, 2025
    • MIT License
      1210Updated Jul 1, 2025Jul 1, 2025
    • Jupyter Notebook
      MIT License
      0000Updated May 29, 2025May 29, 2025
    • Salamander is a non-negative matrix factorization framework for signature analysis
      Python
      MIT License
      0900Updated Aug 30, 2024Aug 30, 2024
    • SigMA

      Public
      Mutational signature analysis for low statistics SNV data
      R
      Other
      2264110Updated Aug 7, 2024Aug 7, 2024
    • MuSiCal

      Public
      A comprehensive toolkit for mutational signature analysis
      Python
      Other
      741110Updated Jul 19, 2024Jul 19, 2024
    • Software program for checking sample matching for NGS data
      Python
      MIT License
      57139294Updated Jun 20, 2024Jun 20, 2024
    • Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data
      Python
      42103Updated Apr 22, 2024Apr 22, 2024
    • Scripts for the glia project
      R
      0010Updated Mar 6, 2024Mar 6, 2024
    • R
      3700Updated Oct 23, 2023Oct 23, 2023
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