CSOgroup/Donaldson-et-al-scripts

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CSOgroup/Donaldson-et-al-scripts

CSOgroup

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A public repository containing the scripts regarding analyses in Donaldson, Sungalee, Zufferey, Tavernari et al.

CALDER

cellcharter

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

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.

TAD-benchmarking-scripts

Repository containing the scripts regarding analyses in Zufferey & Tavernari et al.

scrnaseq_pipeline

GridQuant

Gridding framework for quantification and statistical analyses of spatially-resolved protein expression from high resolution images

CALDER_workflow

Scalable pipeline for the computation of compartment domains based on Hi-C data using CALDER

WGD

Analysis code for "Whole genome doubling drives oncogenic loss of chromatin segregation"

Lymphomoid-IF-pipeline

TLS-finder

A pipeline to detect Tertiary Lymphoid Structures in-situ from CD20 immunofluorescence staining images.