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    18 repositories

    • UrothelialCancer_WGS_paper_figures

      Public
      This repository contains the code necessary for reproducing the figures and custom analysis in the following manuscript: The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated Aug 13, 2025Aug 13, 2025

    • Prostate_WCM63_paper_figures_2025

      Public
      Analysis, figure and code for Prostate WCM63 manuscript.
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • ProstateBrainMet_WGS_paper_figures

      Public
      This repository contains the code necessary for reproducing the figures and custom analysis in the following manuscript: Evolution of Structural Rearrangements in Prostate Cancer Intracranial Metastases
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Aug 13, 2025Aug 13, 2025

    • Lancet2

      Public
      v2.x of the microassembly based somatic variant caller
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •5•24•1•0•Updated Jul 16, 2025Jul 16, 2025

    • nygc-germline-pipeline-readmes

      Public
      NYGC Germline Analysis Pipeline README
      0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • Conpair

      Public
      Concordance and contamination estimator for tumor–normal pairs
      Python
      •
      Other
      •34•60•14•2•Updated Oct 22, 2024Oct 22, 2024

    • telomeasure

      Public
      Telomeasure estimates average telomere length from whole genome sequencing (WGS) BAM files.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•0•Updated May 6, 2024May 6, 2024

    • compass

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 3, 2023Apr 3, 2023

    • lancet

      Public
      Microassembly based somatic variant caller for NGS data
      cancer-genomicssomatic-mutationsindelssnvsdebruijn-graphlocal-assemblyvariant-callers
      C
      •
      Other
      •35•155•0•0•Updated Jun 23, 2022Jun 23, 2022

    • absinthe

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Nov 9, 2021Nov 9, 2021

    • taxmaps

      Public
      Ultra-efficient taxonomic mapping of NGS data
      Python
      •
      Other
      •12•52•0•1•Updated Mar 26, 2021Mar 26, 2021

    • nygc-short-alignment-marking

      Public
      Other
      •0•1•1•0•Updated Nov 25, 2020Nov 25, 2020

    • topmed_unmapped

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Nov 13, 2020Nov 13, 2020

    • metronome

      Public
      Visual Data Exploration for Genomic Medicine
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 31, 2019Jul 31, 2019

    • SCANVIS

      Public
      SCANVIS - a toolkit for SCoring, ANnotating and VISualizing splice junctions
      R
      •
      Other
      •2•8•5•0•Updated Jul 17, 2019Jul 17, 2019

    • nygc-PDX-mouse-read-filter

      Public
      0•0•0•0•Updated Mar 12, 2019Mar 12, 2019

    • cotton

      Public
      A library of useful functions for managing deployments with Fabric.
      Python
      •
      Other
      •2•0•0•0•Updated Jun 12, 2017Jun 12, 2017

    • pedselect

      Public
      Select most informative individuals to sequence from a pedigree
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 30, 2017Mar 30, 2017