README

This is the official repository of the R package SELECT - Selected Events Linked by Evolutionary Conditions across human Tumors - a methodology to infer evolutionary inter-dependencies between functional alterations in cancer.

What is this repository for?

• SELECT is a package for inferring evolutionary dependencies between functional alterations in cancer starting from patterns of alteration occurrences in large tumor sample cohorts.
• Last Version: 1.6.4

How To

• Summary of set up

install.packages("devtools")
devtools::install_github("CSOgroup/select")

• How to use
  • Check the introduction fom vignettes folder or the website.
  • Also refere to methods section of papers to know the best way to apply the method.

Citation

If you use this tool, please cite the papers

• Mina, M., Iyer, A., Tavernari, D., Raynaud, F., & Ciriello, G. (2020). Discovering functional evolutionary dependencies in human cancers Nature Genetics, 52(11), 1198-1207.

• Mina, Marco and Raynaud, Franck and Tavernari, Daniele and Battistello, Elena and Sungalee, Stephanie and Saghafinia, Sadegh and Laessle, Titouan and Sanchez-Vega, Francisco and Schultz, Nikolaus and Oricchio, Elisa and Ciriello, G. (2017). Conditional selection of genomic alterations dictates cancer evolution and oncogenic dependencies. Cancer cell, 32(2), 155-168.

Contribution guidelines

• SELECT was originally developed by Marco Mina at the University of Lausanne, Switzerland.
• SELECT is currently maintained by Arvind Iyer and memeber of the Computational Systems Oncology lab (CSO) at the University of Lausanne (Unil), Switzerland.

Who do I talk to?

• For any bugs or feature support in using SELECT, please use the issue tracker.
• For any other question related to SELECT, please contact Giovanni Ciriello (giovanni.ciriello@unil.ch).