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@CSOgroup Computational Systems Oncology

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    30 repositories

    • torchgmm

      Public
      Python
      •
      MIT License
      •0•3•0•1•Updated Nov 18, 2024Nov 18, 2024

    • egfr_classes

      Public
      Repository containing the code for the EGFR classes study.
      R
      •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • HaploC-tools

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 17, 2024Nov 17, 2024

    • 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
      •3•92•2•0•Updated Nov 12, 2024Nov 12, 2024

    • Lymphomoid-IF-pipeline

      Public
      Python
      •0•1•0•0•Updated Oct 30, 2024Oct 30, 2024

    • SelectSim_analysis

      Public
      Scripts and supplementary material for SelectSim paper.
      Jupyter Notebook
      •0•0•0•0•Updated Oct 5, 2024Oct 5, 2024

    • diffComp

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

    • SelectSim

      Public
      This R package implements the SelectSim methodology to infer evolutionary dependencies between functional alterations in cancer.
      R
      •
      Other
      •0•1•1•0•Updated Aug 27, 2024Aug 27, 2024

    • scrnaseq_pipeline

      Public
      Python
      •0•3•0•0•Updated Aug 7, 2024Aug 7, 2024

    • cellcharter_analyses

      Public
      Jupyter Notebook
      •
      MIT License
      •3•6•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

    • 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•18•2•0•Updated Dec 24, 2023Dec 24, 2023

    • select

      Public
      SELECT - Selected Events Linked by Evolutionary Conditions across human Tumors
      R
      •
      GNU Lesser General Public License v3.0
      •0•3•0•0•Updated Aug 28, 2023Aug 28, 2023

    • .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
      •3•19•5•1•Updated Jul 27, 2023Jul 27, 2023

    • hic_pipeline

      Public
      Bioinformatic pipeline for the analysis of Hi-C data
      Shell
      •0•2•0•0•Updated Jul 7, 2023Jul 7, 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
      •719•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.3k•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•2•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

    • TLS-finder

      Public
      A pipeline to detect Tertiary Lymphoid Structures in-situ from CD20 immunofluorescence staining images.
      Groovy
      •0•1•0•0•Updated Jul 13, 2020Jul 13, 2020

    • Donaldson-et-al-scripts

      Public
      A public repository containing the scripts regarding analyses in Donaldson, Sungalee, Zufferey, Tavernari et al.
      R
      •1•3•0•0•Updated Oct 16, 2019Oct 16, 2019

    • Model_Cancer_Evolution

      Public
      Python
      •0•0•0•0•Updated Aug 26, 2019Aug 26, 2019

    • Raynaud_et_al

      Public
      Python
      •0•0•0•0•Updated Aug 15, 2018Aug 15, 2018

    • ProcSocB

      Public
      model of clonal evolution and simulation results
      Python
      •0•0•0•0•Updated Jun 8, 2018Jun 8, 2018