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@CSOgroup Computational Systems Oncology

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    35 repositories

    • torchgmm

      Public
      Python
      •
      MIT License
      •3•15•1•2•Updated Dec 22, 2025Dec 22, 2025

    • ADA

      Public
      Code for the Advanced Data Analysis course
      0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • cellcharter

      Public
      A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•147•7•2•Updated Dec 8, 2025Dec 8, 2025

    • HaploC-tools

      Public
      R
      •
      MIT License
      •0•3•0•0•Updated Nov 28, 2025Nov 28, 2025

    • consensusTADs

      Public
      Generate Consensus Topologically Associating Domains from Multiple Prediction Tools
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • Lymphomoid-IF-pipeline

      Public
      R
      •0•1•0•0•Updated Oct 9, 2025Oct 9, 2025

    • TAD-benchmarking-2nd

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 8, 2025Oct 8, 2025

    • ButterflyVI

      Public
      Repository for the ButterflyVI methods
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • SelectSim_analysis

      Public
      Scripts and supplementary material for SelectSim paper.
      Jupyter Notebook
      •0•1•0•0•Updated Jul 18, 2025Jul 18, 2025

    • scrnaseq_pipeline

      Public
      Python
      •0•3•0•0•Updated Jul 4, 2025Jul 4, 2025

    • lung_plasticity

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • CALDER2

      Public
      CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each chromatin domain from short-range contacts.
      R
      •
      MIT License
      •2•26•1•0•Updated Apr 16, 2025Apr 16, 2025

    • SelectSim

      Public
      This R package implements the SelectSim methodology to infer evolutionary dependencies between functional alterations in cancer.
      R
      •
      Other
      •0•1•2•0•Updated Apr 4, 2025Apr 4, 2025

    • hic_pipeline

      Public
      Bioinformatic pipeline for the analysis of Hi-C data
      Shell
      •0•2•0•0•Updated Mar 12, 2025Mar 12, 2025

    • egfr_classes

      Public
      Repository containing the code for the EGFR classes study.
      R
      •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

    • select

      Public
      SELECT - Selected Events Linked by Evolutionary Conditions across human Tumors
      R
      •
      GNU Lesser General Public License v3.0
      •0•5•1•0•Updated Nov 26, 2024Nov 26, 2024

    • diffComp

      Public
      Python package for the analysis of differential chromatin compartmentalization
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 23, 2024Sep 23, 2024

    • cellcharter_analyses

      Public
      Jupyter Notebook
      •
      MIT License
      •3•11•1•0•Updated Jun 6, 2024Jun 6, 2024

    • SelectPortal

      Public
      SelectPortal is a hybrid database resource hosting co-mutational results from the TCGA dataset using SELECT, featuring a flexible architecture integrating relational and non-relational database concepts for seamless data extraction and analysis.
      HTML
      •0•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • .github

      Public
      Repository for introduction to CSO group github page.
      0•0•0•0•Updated Aug 25, 2023Aug 25, 2023

    • wgs_pipeline

      Public
      Whole-genome sequencing pipeline
      Shell
      •0•0•0•0•Updated Aug 7, 2023Aug 7, 2023

    • CALDER

      Public
      R
      •
      MIT License
      •5•22•5•1•Updated Jul 27, 2023Jul 27, 2023

    • repliseq_pipeline

      Public
      Bioinformatic pipeline for the analysis of Repli-seq data
      Shell
      •0•1•0•0•Updated Apr 26, 2023Apr 26, 2023

    • nfcore-modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •950•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.7k•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • WGD

      Public
      Analysis code for "Whole genome doubling drives oncogenic loss of chromatin segregation"
      data-sciencerna-seqgenomicsreproducible-researchhi-cchip-seqnaturewhole-genome-sequencingsingle-cell-rna-seqsingle-cell-hic
      Python
      •0•4•0•0•Updated Jan 5, 2023Jan 5, 2023

    • GridQuant

      Public
      Gridding framework for quantification and statistical analyses of spatially-resolved protein expression from high resolution images
      R
      •0•2•0•0•Updated Feb 14, 2022Feb 14, 2022

    • CALDER_workflow

      Public
      Scalable pipeline for the computation of compartment domains based on Hi-C data using CALDER
      Python
      •0•1•0•0•Updated Jan 11, 2022Jan 11, 2022

    • DADo

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jun 30, 2021Jun 30, 2021

    • TAD-benchmarking-scripts

      Public
      Repository containing the scripts regarding analyses in Zufferey & Tavernari et al.
      R
      •
      Other
      •2•10•0•0•Updated Feb 22, 2021Feb 22, 2021