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    13 repositories

    • IPMNPDACpaperArchive

      Public
      Scripts for analyzing IPMN-PDAC multi-region WGS and RNAseq data
      HTML
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      MIT License
      •0•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • battenberg

      Public
      Battenberg R package for subclonal copynumber estimation
      R
      •
      GNU Affero General Public License v3.0
      •61•95•20•2•Updated Feb 20, 2026Feb 20, 2026

    • dpclust3p

      Public
      Dirichlet Process Clustering Pre-Processing Pipeline
      R
      •
      GNU Affero General Public License v3.0
      •13•9•7•1•Updated Feb 20, 2026Feb 20, 2026

    • dpclust

      Public
      Dirichlet Process based methods for subclonal reconstruction of tumours
      R
      •
      GNU Affero General Public License v3.0
      •19•32•6•2•Updated Feb 18, 2026Feb 18, 2026

    • Gel_pan_cancer_signatures

      Public
      Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types from 10,983 cancer patients_doi.org/10.1101/2023.06.07.2…
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•0•11•Updated Dec 29, 2025Dec 29, 2025

    • SpatialPhyloPlot

      Public
      An R package to automate plotting of phylogenetic trees from spatial transcritpomics data.
      HTML
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      GNU General Public License v3.0
      •0•2•0•0•Updated Aug 12, 2025Aug 12, 2025

    • multidimDPClust

      Public
      Runs DPClust for variant clustering at a multi-dimensional level (N ~ 4,5 or above)
      R
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated May 14, 2025May 14, 2025

    • WrapCleanCNA

      Public
      A nextflow pipeline to run CleanCNA
      Nextflow
      •1•0•0•0•Updated Apr 18, 2025Apr 18, 2025

    • AmplificationTimeR

      Public
      Code for timing amplifications
      R
      •
      GNU General Public License v3.0
      •1•5•2•0•Updated Jun 6, 2024Jun 6, 2024

    • AmplificationTimeR_paper_archive

      Public archive
      A repository to store any code that was run as part of the AmplificationTimeR publication.
      HTML
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      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 25, 2024Apr 25, 2024

    • PhaDPClust

      Public
      PhaDPClust
      R
      •0•0•0•0•Updated Nov 27, 2022Nov 27, 2022

    • InUtero_MPN

      Public archive
      Code accompanying 'In utero origin of myelofibrosis presenting in adult monozygotic twins' (Sousos, Ní Leathlobhair, et al., Nature Medicine, 2022). See https:/…
      R
      •0•1•0•0•Updated Aug 1, 2022Aug 1, 2022

    • dpclust_smchet_docker

      Public
      DPClust subclonal architecture calling Docker pipeline for SMC-het
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 4, 2017Jul 4, 2017