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@parklab Park Lab at Harvard Medical School

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    Repositories list

    52 repositories

    • SMaHT_SNV_COLO829BLT50_HAPMAP

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Aug 30, 2026Aug 30, 2026

    • parklab.github.io

      Public
      HTML
      •2•0•0•0•Updated Aug 20, 2026Aug 20, 2026

    • NanoSeq_parkLab

      Public
      Analysis software for Nanorate Sequencing (NanoSeq) experiments -- forked over from Sanger Institute
      C++
      •
      GNU Affero General Public License v3.0
      •15•0•0•0•Updated Aug 16, 2026Aug 16, 2026

    • shao_zhao_2026_nature_perinatal_cnv

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • denovo_retroelements_kids_first

      Public
      Python
      •0•0•0•0•Updated Jul 19, 2026Jul 19, 2026

    • Sonata

      Public
      Python toolkit for mutational signature analysis using NMF algorithms.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2026Jun 2, 2026

    • EchoSV

      Public
      A novel tool for accurately merging haplotype-based SV calls and comparing SVs across reference genomes
      cross-referencegenotypingsv-merging
      cross-referencegenotypingsv-mergingsv-comparison
      Python
      •
      MIT License
      •0•6•0•0•Updated May 19, 2026May 19, 2026

    • zhou_luquette_2026_genomic_damage_in_neurodegeneration

      Public
      Scripts to recreate analyses in Zhou, Luquette et al. Cell 2026.
      Shell
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • reference_genomes_decoy_analysis

      Public
      Scripts to analyze read alignment and variant calling from simulated and empirical data based on different human reference genome versions.
      Shell
      •0•0•0•0•Updated May 4, 2026May 4, 2026

    • xTea

      Public
      Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
      nanoporepacbioillumina
      nanoporepacbioilluminatransposable-elementslinked-readsmobile-element-insertion
      Python
      •
      Other
      •24•128•13•2•Updated Apr 17, 2026Apr 17, 2026

    • Illumina-TwoColorBias

      Public
      A repository containing code to correct T>N mutation bias in NovaSeq 6000 callsets
      Jupyter Notebook
      •0•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • SMaHT_Regional_Categorization

      Public
      This repository has the description of the hg38 genome categorization of easy, difficult, and extreme region.
      0•2•0•0•Updated Feb 25, 2026Feb 25, 2026

    • SMaHT_Tissue_Benchmark_SmallVariants

      Public
      0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • KidsFirst_TE_pediatric_cancer

      Public
      R
      •0•1•0•0•Updated Jan 29, 2026Jan 29, 2026

    • MosaicForecast

      Public
      A mosaic detecting software based on phasing and random forest
      Python
      •
      MIT License
      •21•71•7•2•Updated Dec 8, 2025Dec 8, 2025

    • code-share

      Public
      Repository to host shared code for the lab
      Shell
      •0•1•0•0•Updated Nov 10, 2025Nov 10, 2025

    • spatial_sampling_analysis

      Public
      This repository contains analysis of spatially-resolved somatic mutations datasets.
      HTML
      •
      MIT License
      •0•1•0•0•Updated Sep 17, 2025Sep 17, 2025

    • r-scan2

      Public
      R package supporting the SCAN2 pipeline
      R
      •5•0•2•0•Updated Aug 26, 2025Aug 26, 2025

    • HiScanner

      Public
      C
      •
      MIT License
      •2•9•1•0•Updated Aug 13, 2025Aug 13, 2025

    • bamsnap

      Public
      HTML
      •
      MIT License
      •29•127•22•0•Updated Aug 1, 2025Aug 1, 2025

    • SPECIFICANCER_data

      Public
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated 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
      •9•23•18•1•Updated Jul 28, 2025Jul 28, 2025

    • ViScanner

      Public
      Scanner output visualization tool
      JavaScript
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • r-mutenrich

      Public
      Analyze distribution of somatic mutations with permutations as a background
      R
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • hiscanner_demo

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

    • Salamander

      Public
      Salamander is a non-negative matrix factorization framework for signature analysis
      Python
      •
      MIT License
      •0•9•0•0•Updated Aug 30, 2024Aug 30, 2024

    • SigMA

      Public
      Mutational signature analysis for low statistics SNV data
      R
      •
      Other
      •21•66•11•0•Updated Aug 7, 2024Aug 7, 2024

    • MuSiCal

      Public
      A comprehensive toolkit for mutational signature analysis
      Python
      •
      Other
      •7•42•12•0•Updated Jul 19, 2024Jul 19, 2024

    • NGSCheckMate

      Public
      Software program for checking sample matching for NGS data
      Python
      •
      MIT License
      •57•143•30•4•Updated Jun 20, 2024Jun 20, 2024

    • MSIprofiler

      Public
      Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data
      Python
      •4•21•0•3•Updated Apr 22, 2024Apr 22, 2024
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