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beyondcell

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

bollito

A single-cell RNA-seq pipeline

breast-bcspatial

Code used to produce the final figures and tables of the study "Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity".

bu-website-merge_fork

cluster_rnaseq

cnio-bu.github.io

Source code for generating https://cnio-bu.github.io

drug_susceptibility_collection

A snakemake pipeline to generate the transcriptomic signatures of drug susceptibility used in beyondcell

gotcha

Pipeline for processing of GoT-ChA genotyping data and downstream analysis

myelong

ngs-test-data

pandrugs-db

protter

sc-test-data

ssc-breast

A snakemake pipeline to generate the transcriptomic signatures of breast cancer drug susceptibility used in "Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity".

st-preprocess

Pipelines to preprocess 10x Visium data, including spot filtering and deconvolution, normalization and beyondcell score calculation.

varca

vulcanspot

vulcanspot-ui

vulcanspot_ui

website