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    39 repositories

    • deepUMIcaller

      Public
      A Nextflow pipeline for duplex sequencing data analysis
      nextflowvariant-callingduplex-sequencing
      Nextflow
      •
      Other
      •2•2•30•3•Updated Jan 5, 2026Jan 5, 2026

    • deepCSA

      Public
      Pipeline for the analysis of the clonal structure of tissues. It takes advantage of the availability of information about the sequencing depth.
      Python
      •
      Other
      •0•1•115•2•Updated Jan 5, 2026Jan 5, 2026

    • bbgregressions

      Public
      Code to run linear models for association analysis
      Python
      •
      Other
      •0•0•7•0•Updated Dec 22, 2025Dec 22, 2025

    • cancer-detective-pro

      Public
      Cancer Detective activity
      HTML
      •0•0•14•0•Updated Dec 17, 2025Dec 17, 2025

    • wetdry-metrics

      Public
      Compilation of duplex sequencing metrics
      Python
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • oncodrive3d

      Public
      A computational approach for identifying cancer driver genes by detecting three-dimensional clusters of somatic missense mutations in protein structures.
      Python
      •
      Other
      •0•4•8•0•Updated Dec 16, 2025Dec 16, 2025

    • omega

      Public
      dN/dS analysis
      Python
      •
      Other
      •0•2•18•1•Updated Dec 10, 2025Dec 10, 2025

    • bbgwiki

      Public
      Website with info of all the tools and data used in the bbglab
      HTML
      •2•4•50•2•Updated Dec 5, 2025Dec 5, 2025

    • openvariant

      Public
      read, parse and operate different multiple input file formats with OpenVariant
      pythonbioinformaticsopenvariantbbglabopenvar
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•14•3•1•Updated Nov 28, 2025Nov 28, 2025

    • SpotNeoMet

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • cgi-clinics-api

      Public
      This repository contains python scripts to serve as a guide on how to use the CGI-Clinics API.
      Python
      •0•4•1•0•Updated Oct 10, 2025Oct 10, 2025

    • containers

      Public archive
      Dockerfile
      •1•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • containers-recipes

      Public
      Dockerfile
      •1•0•2•0•Updated Sep 8, 2025Sep 8, 2025

    • HDP_sigExtraction

      Public
      Pipeline to extract de novo mutational signatures using HDP.
      R
      •
      MIT License
      •1•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • intogen-plus

      Public
      a framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients.
      Python
      •
      Other
      •3•6•8•1•Updated Aug 8, 2025Aug 8, 2025

    • oncodrive3d_paper

      Public
      Analysis performed for the publication of Oncodrive3D.
      Jupyter Notebook
      •0•1•0•0•Updated Jul 22, 2025Jul 22, 2025

    • normal_bladder_paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • boostdm-pipeline

      Public
      Learning pipeline to identify somatic SNVs under positive selection.
      Python
      •
      Other
      •0•5•12•0•Updated Jun 25, 2025Jun 25, 2025

    • rasp_cpu

      Public
      Python
      •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • qmap

      Public
      A tool to run a collection of similar jobs quickly and easily in parallel. It can run standalone or using different HPC schedulers (Slurm, Sun Grid Engine...)
      Python
      •
      Other
      •0•1•2•0•Updated Apr 22, 2025Apr 22, 2025

    • randomize-mutations

      Public
      Utils for simple mutation randomization based on trinucleotide context specific mutation rate
      Jupyter Notebook
      •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • oncodrivefml

      Public
      Python
      •
      Other
      •1•5•9•0•Updated Jan 25, 2025Jan 25, 2025

    • boostdm-analyses

      Public
      Source code to reproduce the figures of the boostDM paper
      mutationsdriverscancer-genes
      Jupyter Notebook
      •
      MIT License
      •3•6•0•0•Updated Dec 17, 2024Dec 17, 2024

    • oncodriveclustl

      Public
      Python
      •
      Other
      •0•5•4•0•Updated Dec 13, 2024Dec 13, 2024

    • immunebiomarkers

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 13, 2024Aug 13, 2024

    • smregions

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • hartwig_biomarkers

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 2, 2024Aug 2, 2024

    • second-tumors-children

      Public
      This repository contains the necessary code to reproduce the analysis of "Origins of Second Malignancies in Children and Mutational Footprint of Chemotherapy in Normal Tissues"
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

    • hotspot_propensity

      Public
      Source code to reproduce hotspot propensity analyses and figures
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Dec 21, 2023Dec 21, 2023

    • cancer-detective

      Public
      A simulation to learn about cancer and mutations, based on Cancer Genome Interpreter
      genomicsgenomecancer-genomicscancer-research
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated May 3, 2023May 3, 2023