DESCRIPTION

Package: Bioc2017.TCGAbiolinks.ELMER
Title: Bioc2017.TCGAbiolinks.ELMER
Version: 0.0.0.9000
Authors@R: person("Tiago", "Chedraoui Silva", email = "tiagochst@gmail.com", role = c("aut", "cre"))
Description: In this workshop, we will use the R/Bioconductor 
    TCGAbiolinks package to search and download DNA methylation (epigenetic) 
    and gene expression (transcription) data from the newly 
    created NCI Genomic Data Commons (GDC) portal and prepare 
    them into a Summarized Experiment object. We will introduce 
    the workflow using our recently developed TCGAbiolinks and if time 
    permitted, we will highlight the Graphics User Interface 
    version (TCGAbiolinksGUI). 
    This data will be used to performa an integrative analysis using
    the R/Bioconductor ELMER package (version 2.0) which allows 
    one to identify DNA methylation changes in distal regulatory 
    regions and correlate these signatures with expression of nearby genes 
    to identify transcriptional targets associated with cancer. 
    For these distal probes correlated 
    with a gene, a transcription factor motif analysis is performed 
    followed by expression analysis of transcription factors 
    to infer upstream regulators.
    We expect that participants of this workshop will 
    understand the integrative analysis performed by using TCGAbiolinks + ELMER, 
    as well as be able to execute it from the data acquisition process to the 
    final interpretation of the results. 
    The workshop assumes users with an intermediate level of familiarity with R, 
    and basic understanding of tumor biology. 
Depends: R (>= 3.4.0)
Suggests:
  TCGAbiolinks (>= 2.5.5),
  TCGAbiolinksGUI (>= 1.3.0),
  DT,
  dplyr,
  ELMER (>= 2.0.1),
  knitr,
  rmarkdown
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr