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README.md

CELLector: Genomics Guided Selection of Cancer in vitro models

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Najgebauer, H., Yang, M., Francies, H., Stronach, E. A., Garnett, M. J., Saez-Rodriguez, J., & Iorio, F. (n.d.). CELLector: Genomics Guided Selection of Cancer in vitro Models. http://doi.org/10.1101/275032

2018-04-14 CELLector is a computational tool to assist the selection of the most relevant cancer cell lines to be included in a new in-vitro study (or to be considered in a retrospective study) in a genomic-guided fashion. CELLector combines methods from graph theory and market basket analysis; it leverages tumour genomics data to explore, rank, and select optimal cell line models in a user-friendly way, enabling scientists to make appropriate and informed choices about model inclusion/exclusion in retrospective analyses and future studies. Additionally, it allows the selection of models within user-defined contexts, for example, by focusing on genomic alterations occurring in biological pathways of interest or considering only predetermined sub-cohorts of cancer patients. Finally, CELLector identifies combinations of molecular alterations underlying disease subtypes currently lacking representative cell lines, providing guidance for the future development of new cancer models.

License: MIT

Running Modalities

CELLector can be used in three different modalities:

A tutorial on how to use the online Rshiny app (containing also instruction on how to run it locally) is available here: https://www.biorxiv.org/highwire/filestream/92891/field_highwire_adjunct_files/0/275032-1.pdf

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R package: quick start (interactive vignette)

http://rpubs.com/francescojm/CELLector

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