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    21 repositories

    • mutect_filter

      Public
      Filter based on mutect flags - wave the white flag of surrender
      C++
      •0•0•0•0•Updated Jun 30, 2026Jun 30, 2026

    • DepthOfCoverage

      Public
      R
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • NuclearHorizontalTransfer

      Public
      Code accompanying "Horizontal transfer of nuclear DNA in a transmissible cancer"
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

    • CopyWright

      Public
      Skilled manufacturer of copy number variant calls
      0•0•0•0•Updated Nov 10, 2022Nov 10, 2022

    • rectanglePacking

      Public
      R package for plotting linear segments with position information (e.g. genomic reads), placing them into layers with no overlaps
      C++
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 29, 2022Apr 29, 2022

    • TCG_2020_devil_paper

      Public
      R
      •0•0•0•0•Updated Nov 22, 2020Nov 22, 2020

    • dftdLowCov

      Public
      R package of code relevant to DFTD project
      R
      •0•0•0•0•Updated May 28, 2020May 28, 2020

    • Mixed

      Public
      Repo of simple scripts used by TCG
      C++
      •1•0•0•0•Updated Apr 8, 2020Apr 8, 2020

    • cn_caller

      Public
      Call copy numbers from logR on segmented data
      R
      •1•0•0•0•Updated Mar 2, 2020Mar 2, 2020

    • telseq

      Public
      A software for calculating telomere length
      C++
      •
      GNU General Public License v3.0
      •29•0•0•0•Updated Feb 10, 2020Feb 10, 2020

    • dice

      Public
      Simulation of mutation collision problem
      C++
      •0•0•0•0•Updated Dec 7, 2018Dec 7, 2018

    • ac

      Public
      Basic alleleCounter implementation
      D
      •
      MIT License
      •1•0•0•0•Updated Oct 25, 2018Oct 25, 2018

    • pcr_scanner

      Public
      Scans SAM entries for reads matching a pair of PCR primers
      Python
      •0•1•0•0•Updated May 25, 2018May 25, 2018

    • SNV-filters

      Public
      Somatypus post-processing pipeline
      R
      •0•0•0•0•Updated May 12, 2018May 12, 2018

    • vaf_simulator

      Public
      Shiny app to explore tumour VAF distributions for different copy number states
      R
      •0•0•0•0•Updated Apr 12, 2018Apr 12, 2018

    • poissonProcess

      Public
      Model to estimate time to origin of CTVT from direct transmission data
      R
      •0•0•0•0•Updated Feb 22, 2018Feb 22, 2018

    • vcfToFasta

      Public
      Convert SNP data in a somatypus VCF file to an alignment in Fasta format
      D
      •1•0•0•0•Updated Sep 19, 2017Sep 19, 2017

    • pisa

      Public
      Prototype Integrated Sequence Assembler
      C++
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 11, 2017Sep 11, 2017

    • bamtools

      Public
      C++ API & command-line toolkit for working with BAM data
      C++
      •
      MIT License
      •154•0•0•0•Updated Feb 24, 2017Feb 24, 2017

    • BRASS

      Public
      Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.
      Perl
      •
      GNU Affero General Public License v3.0
      •20•0•0•0•Updated Nov 18, 2016Nov 18, 2016

    • lumpy-sv

      Public
      lumpy: a general probabilistic framework for structural variant discovery
      C
      •
      MIT License
      •115•0•0•0•Updated Sep 26, 2016Sep 26, 2016
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