Analysis of patient-derived xenograft (PDX) data

Contains set of functions to perform analysis of patient-derived xenograft (PDX) data.

methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader

GeneExpression, Pharmacogenetics, Pharmacogenomics,
Software, Classification

A workshop on discovering biomarkers from high through put
response screens

Petr Smirnov, Chris Eeles, Arvind Mer, Benjamin Haibe-Kains

This workshop focuses on the synergies between analysis results 
    from the PharmacoGx, Xeva and RadioGx packages and their usefulness for 
    discovery of biomarkers of drug and/or radiation sensitivity in cancer cell 
    lines (CCLs) and patent derived xenograft models (PDXs).

PharmacoGx, RadioGx, SummarizedExperiment, ToxicoGx, ggplot2,
Xeva, igraph, pkgdown

Analysis of Large-Scale Radio-Genomic Data

c(
  person("Venkata","Manem", email = "mail2mvskumar@gmail.com", 
    role = c("aut")),
  person("Petr","Smirnov", email = "petr.smirnov@uhnresearch.ca", 
    role = c("aut")),
  person("Ian","Smith", email = "ianc.smith@mail.utoronto.ca", 
    role = c("aut")),
  person("Meghan","Lambie", email = "megan.lambie@mail.utoronto.ca", 
    role = c("aut")),
  person("Christopher","Eeles", email = "christopher.eeles@uhnresearch.ca",
    role = c("aut")),
  person("Scott", "Bratman", email = "scott.bratman@rmp.uhn.ca", 
    role = c("aut")),
  person("Benjamin","Haibe-Kains", email = "benjamin.haibe.kains@utoronto.ca",
    role = c("aut","cre"))
  )

Computational tool box for radio-genomic analysis which integrates
    radio-response data, radio-biological modelling and comprehensive cell line
    annotations for hundreds of cancer cell lines. The 'RadioSet' class enables
    creation and manipulation of standardized datasets including information
    about cancer cells lines, radio-response assays and dose-response indicators. 
    Included methods allow fitting and plotting dose-response data using 
    established radio-biological models along with quality control to validate
    results. Additional functions related to fitting and plotting dose response 
    curves, quantifying statistical correlation and calculating area under the
    curve (AUC) or survival fraction (SF) are included. For more details please 
    see the included documentation, references, as well as:
    Manem, V. et al (2018) <doi:10.1101/449793>.