Computational Systems Oncology
CSO lab integrates algorithmic design, numerical modeling, and molecular biology approaches to address relevant questions in cancer biology and therapeutics.
Switzerland
Pinned Repositories
CALDER
CALDER2
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.
cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
cellcharter_analyses
Donaldson-et-al-scripts
A public repository containing the scripts regarding analyses in Donaldson, Sungalee, Zufferey, Tavernari et al.
GridQuant
Gridding framework for quantification and statistical analyses of spatially-resolved protein expression from high resolution images
scrnaseq_pipeline
select
SELECT - Selected Events Linked by Evolutionary Conditions across human Tumors
TAD-benchmarking-scripts
Repository containing the scripts regarding analyses in Zufferey & Tavernari et al.
WGD
Analysis code for "Whole genome doubling drives oncogenic loss of chromatin segregation"
Computational Systems Oncology's Repositories
CSOgroup/cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
CSOgroup/CALDER
CSOgroup/CALDER2
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.
CSOgroup/TAD-benchmarking-scripts
Repository containing the scripts regarding analyses in Zufferey & Tavernari et al.
CSOgroup/cellcharter_analyses
CSOgroup/Donaldson-et-al-scripts
A public repository containing the scripts regarding analyses in Donaldson, Sungalee, Zufferey, Tavernari et al.
CSOgroup/scrnaseq_pipeline
CSOgroup/select
SELECT - Selected Events Linked by Evolutionary Conditions across human Tumors
CSOgroup/torchgmm
CSOgroup/GridQuant
Gridding framework for quantification and statistical analyses of spatially-resolved protein expression from high resolution images
CSOgroup/hic_pipeline
Bioinformatic pipeline for the analysis of Hi-C data
CSOgroup/WGD
Analysis code for "Whole genome doubling drives oncogenic loss of chromatin segregation"
CSOgroup/CALDER_workflow
Scalable pipeline for the computation of compartment domains based on Hi-C data using CALDER
CSOgroup/Lymphomoid-IF-pipeline
CSOgroup/repliseq_pipeline
Bioinformatic pipeline for the analysis of Repli-seq data
CSOgroup/SelectSim
This R package implements the SelectSim methodology to infer evolutionary dependencies between functional alterations in cancer.
CSOgroup/TLS-finder
A pipeline to detect Tertiary Lymphoid Structures in-situ from CD20 immunofluorescence staining images.
CSOgroup/bioconda-recipes
Conda recipes for the bioconda channel.
CSOgroup/DADo
CSOgroup/egfr_classes
Repository containing the code for the EGFR classes study.
CSOgroup/nfcore-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
CSOgroup/ProcSocB
model of clonal evolution and simulation results
CSOgroup/.github
Repository for introduction to CSO group github page.
CSOgroup/diffComp
Python package for the analysis of differential chromatin compartmentalization
CSOgroup/HaploC-tools
CSOgroup/Model_Cancer_Evolution
CSOgroup/Raynaud_et_al
CSOgroup/SelectPortal
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.
CSOgroup/SelectSim_analysis
Scripts and supplementary material for SelectSim paper.
CSOgroup/wgs_pipeline
Whole-genome sequencing pipeline