Repositories list

• 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• SMaHT_SNV_COLO829BLT50_HAPMAP

  Public
  Jupyter Notebook

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• Illumina-TwoColorBias

  Public
  A repository containing code to correct T>N mutation bias in NovaSeq 6000 callsets

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• parklab.github.io

  Public
  HTML

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• NanoSeq_parkLab

  Public
  Analysis software for Nanorate Sequencing (NanoSeq) experiments -- forked over from Sanger Institute

  C++

  •

  GNU Affero General Public License v3.0

  •1515 forks•00 stars•00 issues•00 pull requests•Updated Apr 2, 2026Apr 2, 2026

• xTea

  Public
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

  nanoporepacbioillumina+ 3

  nanoporepacbioilluminatransposable-elementslinked-readsmobile-element-insertion

  Python

  •

  Other

  •2424 forks•124124 stars•1313 issues•22 pull requests•Updated Mar 10, 2026Mar 10, 2026

• SMaHT_Regional_Categorization

  Public
  This repository has the description of the hg38 genome categorization of easy, difficult, and extreme region.

  00 forks•11 star•00 issues•00 pull requests•Updated Feb 25, 2026Feb 25, 2026

• SMaHT_Tissue_Benchmark_SmallVariants

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• KidsFirst_TE_pediatric_cancer

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 29, 2026Jan 29, 2026

• denovo_retroelements_kids_first

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 9, 2026Jan 9, 2026

• MosaicForecast

  Public
  A mosaic detecting software based on phasing and random forest

  Python

  •

  MIT License

  •2121 forks•7070 stars•77 issues•22 pull requests•Updated Dec 8, 2025Dec 8, 2025

• code-share

  Public
  Repository to host shared code for the lab

  Shell

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 10, 2025Nov 10, 2025

• EchoSV

  Public
  A novel tool for accurately merging haplotype-based SV calls and comparing SVs across reference genomes

  cross-referencegenotypingsv-merging+ 1

  cross-referencegenotypingsv-mergingsv-comparison

  Python

  •

  MIT License

  •00 forks•66 stars•00 issues•00 pull requests•Updated Oct 9, 2025Oct 9, 2025

• spatial_sampling_analysis

  Public
  This repository contains analysis of spatially-resolved somatic mutations datasets.

  HTML

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 17, 2025Sep 17, 2025

• r-scan2

  Public
  R package supporting the SCAN2 pipeline

  R

  •44 forks•00 stars•22 issues•00 pull requests•Updated Aug 26, 2025Aug 26, 2025

• HiScanner

  Public
  C

  •

  MIT License

  •22 forks•88 stars•33 issues•00 pull requests•Updated Aug 13, 2025Aug 13, 2025

• bamsnap

  Public
  HTML

  •

  MIT License

  •2929 forks•125125 stars•2020 issues•00 pull requests•Updated Aug 1, 2025Aug 1, 2025

• SPECIFICANCER_data

  Public
  JavaScript

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•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

  •99 forks•1717 stars•1717 issues•11 pull request•Updated Jul 28, 2025Jul 28, 2025

• ViScanner

  Public
  Scanner output visualization tool

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 15, 2025Jul 15, 2025

• r-mutenrich

  Public
  Analyze distribution of somatic mutations with permutations as a background

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 7, 2025Jul 7, 2025

• hiscanner_demo

  Public
  MIT License

  •11 fork•22 stars•11 issue•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• NMF_jointMU

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2025May 29, 2025

• Salamander

  Public
  Salamander is a non-negative matrix factorization framework for signature analysis

  Python

  •

  MIT License

  •00 forks•99 stars•00 issues•00 pull requests•Updated Aug 30, 2024Aug 30, 2024

• SigMA

  Public
  Mutational signature analysis for low statistics SNV data

  R

  •

  Other

  •2222 forks•6464 stars•1111 issues•00 pull requests•Updated Aug 7, 2024Aug 7, 2024

• MuSiCal

  Public
  A comprehensive toolkit for mutational signature analysis

  Python

  •

  Other

  •77 forks•4141 stars•1111 issues•00 pull requests•Updated Jul 19, 2024Jul 19, 2024

• NGSCheckMate

  Public
  Software program for checking sample matching for NGS data

  Python

  •

  MIT License

  •5757 forks•139139 stars•2929 issues•44 pull requests•Updated Jun 20, 2024Jun 20, 2024

• MSIprofiler

  Public
  Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data

  Python

  •44 forks•2121 stars•00 issues•33 pull requests•Updated Apr 22, 2024Apr 22, 2024

• luquette-glia-analysis

  Public
  Scripts for the glia project

  R

  •00 forks•00 stars•11 issue•00 pull requests•Updated Mar 6, 2024Mar 6, 2024

• focal-amplification

  Public
  R

  •33 forks•77 stars•00 issues•00 pull requests•Updated Oct 23, 2023Oct 23, 2023