Najgebauer, H., Yang, M., Francies, H., Pacini, C., Stronach, E. A., Garnett, M. J., Saez-Rodriguez, J., & Iorio, F. CELLector: Genomics Guided Selection of Cancer in vitro Models. http://doi.org/10.1101/275032
2020-03-03
CELLector App is a user friendly interface to CELLector: a computational tool assisting experimental scientists in the selection of the most clinically relevant cancer cell lines to be included in a new in-vitro study (or to be considered in a retrospective study), in a patient-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, through the CELLector Rshiny App. This enables making appropriate and informed choices about model inclusion/exclusion in retrospective analyses, future studies and it makes possible bridging cancer patient genomics with public available databases froom cell line based functional/pharmacogenomic screens, such as CRISPR-cas9 dependency datasets and large-scale in-vitro drug screens.
Furthermore, CELLector includes interface functions to synchronise built-in cell line annotations and genomics data to their latest versions from the Cell Model Passports resource. Through this interface, bioinformaticians can quickly generate binary genomic event matrices (BEMs) accounting for hundreds of cancer cell lines, which can be used in systematic statistical inferences, associating patient-defined cell line subgroups with drug-response/gene-essentiality, for example through GDSC tools.
Additionally, CELLector 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: GNU GPLv3
CELLector can be used in three different modalities:
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(i) as an R package (within R, code available at: https://github.com/francescojm/CELLector) Package vignette
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(ii) as an online R shiny App (available at: https://ot-cellector.shinyapps.io/CELLector_App/)
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(iii) as a local R shiny App (within Rstudio, code available at: https://github.com/francescojm/CELLector_App)
[Shiny App tutorial and use cases](link to be added)