EMT

This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons et al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI.

This workshop presents our vissE tool and shows how protein-protein interaction networks derived from it can be further interpreted using the Cytoscape network analysis tool.

vissE is a tool that can help identify, visualise and explore higher-order biological processes from the results of a gene-set enrichment analysis (GSEA)

A workshop on using vissE to analyse transcriptomic data

A talk on using vissE to analyse transcriptomic data

This masterclass includes an introductory lecture on gene-set enrichment analysis followed by a demonstration of the vissE and singscore tools we developed.

A talk on the inner workings of vissE

This workshop demonstrates a workflow for single-sample gene-set enrichment analysis.

singscore is a robust rank-based method to compute molecular phenotypes scores for individual samples such as those originating from an individual patient in the clinic