siMEM algorithm R code

Manuscript

"Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities and Resistance"

Richard Marcotte*, Azin Sayad*, Kevin R. Brown, Felix Sanchez-Garcia, Jüri Reimand, Maliha Haider, Carl Virtanen, James E. Bradner, Gary D. Bader, Gordon B. Mills, Dana Pe’er, Jason Moffat and Benjamin G. Neel
Cell, Volume 164, Issues 1–2, 14 January 2016, Pages 293–309

(* Equal Contributions)

Cell | PubMed | Science Direct
Data Website

News/Updates

• 2016-07-05:
  • New Cowley et al. 2014 Project Achilles analysis example: 2 class ovarian vs. other cancer context-specific essentiality (listed under Tutorial, or click HERE)
  
  
  • New Cheung et al. 2011 Project Achilles analysis example: per-gene continuous expression vs. essentiality (listed under Tutorial, or click HERE)
  
  
  • Added an easy to download zip bundle containing all siMEM R files. You can download the code zip file HERE
  
  
  • Added the option to download each tutorial as an R file for easy use.
  
  
  • Updates to siMEM code, most notably to switch parallelization code from the doMC R package to doParallel, so that Windows is now also supported.
  
  
  • Download links to all screen datasets used in tutorials at the bottom of this page for easier access. Links can also be found in each tutorial.
  
  
• 2016-01-14: Manuscript, data and siMEM code published.
  
  

R Code

• Download all siMEM R code files bundled in a zip file
• On GitHub
• Bioconductor package: In Progress

Tutorial

• Assign Precision Weights to Measurements


• Use case examples:
  
  
  • 2 class context-specific essentiality: Breast HER2+ example
  
  
  • Essentiality with continuous expression: Breast CCND1 expression example
  
  
  • Essentiality vs. continuous expression (per-gene): Cheung 2011 Project Achilles example
  
  
  • 2 class context-specific essentiality: Cowley 2014 Project Achilles Ovarian vs. Other Cancer example


• Download links
  Screen datasets formatted as R ExpressionSets for use with the siMEM algorithm code. These ExpressionSets include precision weights and, for the Marcotte 2016 screens, signal-noise weights:
  
  
  • Marcotte et al. 2016 Breast screens (77 screens, measured by microarray) - DOWNLOAD
  
  
  • Cheung et al. 2011 Project Achilles multi-tissue screens (~100 screens, measured by microarray) - DOWNLOAD
  
  
  • Cowley et al. 2014 Project Achilles multi-tissue screens (~200 screens, expanded from Cheung 2011, measured by sequencing) - DOWNLOAD