Repositories list

• website

  Public
  0•0•0•1•Updated Oct 3, 2024Oct 3, 2024

• SPECIFICANCER_data

  Public
  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• Salamander

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

  Python

  •

  MIT License

  •0•8•0•0•Updated Aug 30, 2024Aug 30, 2024

• denovo_retroelements_kids_first

  Public
  0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

• SigMA

  Public
  Mutational signature analysis for low statistics SNV data

  R

  •

  Other

  •21•62•10•0•Updated Aug 7, 2024Aug 7, 2024

• SCAN2

  Public
  SCAN2 is a somatic SNV and indel genotyper for single cells amplified by Primary Template-Directed Amplification (PTA)

  Python

  •5•10•12•0•Updated Aug 3, 2024Aug 3, 2024

• MuSiCal

  Public
  A comprehensive toolkit for mutational signature analysis

  Python

  •

  Other

  •5•31•1•0•Updated Jul 19, 2024Jul 19, 2024

• xTea

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

  nanoporepacbioillumina+ 3transposable-elementslinked-readsmobile-element-insertion

  Python

  •

  Other

  •23•99•9•3•Updated Jun 27, 2024Jun 27, 2024

• NGSCheckMate

  Public
  Software program for checking sample matching for NGS data

  Python

  •

  MIT License

  •47•123•26•3•Updated Jun 20, 2024Jun 20, 2024

• r-scan2

  Public
  R package supporting the SCAN2 pipeline

  R

  •3•0•1•0•Updated May 22, 2024May 22, 2024

• MSIprofiler

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

  Python

  •4•20•0•3•Updated Apr 22, 2024Apr 22, 2024

• HiScanner

  Public
  C

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  MIT License

  •0•4•1•0•Updated Apr 11, 2024Apr 11, 2024

• code-share

  Public
  Repository to host shared code for the lab

  Shell

  •0•0•0•0•Updated Mar 12, 2024Mar 12, 2024

• luquette-glia-analysis

  Public
  Scripts for the glia project

  R

  •0•0•0•0•Updated Mar 6, 2024Mar 6, 2024

• ViScanner

  Public
  Scanner output visualization tool

  JavaScript

  •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

• focal-amplification

  Public
  R

  •3•7•0•0•Updated Oct 23, 2023Oct 23, 2023

• SVA_catalog

  Public
  Host the SVA reference catalog

  JavaScript

  •0•0•0•0•Updated Sep 16, 2023Sep 16, 2023

• SVA_landscape_project

  Public
  HTML

  •0•0•1•0•Updated Sep 16, 2023Sep 16, 2023

• MosaicForecast

  Public
  A mosaic detecting software based on phasing and random forest

  Python

  •

  MIT License

  •21•61•5•4•Updated Sep 6, 2023Sep 6, 2023

• ShatterSeek

  Public
  TeX

  •23•65•5•1•Updated Jul 12, 2023Jul 12, 2023

• mutagenesis_tools

  Public
  Scripts for simulating mutant peptides and reading frames from mutations

  Python

  •0•1•0•0•Updated Nov 14, 2022Nov 14, 2022

• scan-snv

  Public
  Single cell somatic genotyper

  Python

  •5•9•6•0•Updated Sep 28, 2022Sep 28, 2022

• r-mutenrich

  Public
  Analyze distribution of somatic mutations with permutations as a background

  R

  •0•0•0•0•Updated Jul 9, 2022Jul 9, 2022

• SCAN2_PTA_paper_2022

  Public
  Scripts for replicating the analyses in Luquette et al. 2022

  R

  •0•3•0•0•Updated May 9, 2022May 9, 2022

• LiRA

  Public
  R

  •4•18•5•1•Updated Feb 25, 2022Feb 25, 2022

• bamsnap

  Public
  HTML

  •

  MIT License

  •24•111•20•2•Updated Nov 24, 2021Nov 24, 2021

• mpnst_surveyor

  Public
  R

  •1•0•0•0•Updated Aug 11, 2021Aug 11, 2021

• HiNT

  Public
  HiC for copy Number variation and Translocation detection

  Python

  •

  MIT License

  •8•35•21•0•Updated Aug 4, 2021Aug 4, 2021

• xTea_paper

  Public
  Host the scripts, running commands, and results for the xTea paper.

  Jupyter Notebook

  •1•2•0•0•Updated Jul 16, 2021Jul 16, 2021

• kras_project

  Public
  JavaScript

  •2•0•0•0•Updated Jun 10, 2021Jun 10, 2021