Download

Package source

coga_0.01-1.tar.gz

Windows binaries

coga_0.01-1.zip

Mac OS X binaries

coga_0.01-1.tgz

Installation

Dependencies

R (>= 3.0.0), shiny (>= 0.8.0), WGCNA, igraph, shinyBS, RColorBrewer, Hmisc, psych, RJSONIO, whisker, yaml, pheatmap, preprocessCore, GO.db, AnnotationDbi, impute, and ggplot2

Installation steps

  1. If don't have the R software installed in our computer, download and install it (check out the R home page: http://www.r-project.org/)
  2. Download the CoGA package
  3. Open the R command line interface, and install all CoGA dependencies (if they have not been installed yet):
    $ source("http://bioconductor.org/biocLite.R")
    $ biocLite("impute")
    $ biocLite("preprocessCore")
    $ biocLite("GO.db")
    $ biocLite("AnnotationDbi")
    $ install.packages(c("WGCNA", "igraph", "RColorBrewer", "Hmisc", "psych", "RJSONIO", "whisker", "yaml", "pheatmap", "ggplot2"))
    Please, install versions 0.8.0 and 0.20 for shiny and shinyBS, respectively. We are working to make the CoGA package compatible with the new versions of the packages as soon as possible. To install the recommended versions for shiny and shinyBS, just type the following commands on the R command-line:
    $ install.packages("devtools")
    $ devtools::install_version("shiny", "0.8.0")
    $ devtools::install_version("shinyBS", "0.20")
  4. Install the CoGA package:
    $ install.packages(path_of_the_downloaded_file)
    For example, if you use Linux and save the CoGA package at your Desktop, you would probably do: install.packages("~/Desktop/coga_0.01-1.tar.gz")
  5. To run CoGA, just type the following code:
    library(coga)
    runCoga()
  6. Wait for the browser page to open, and enjoy CoGA!

Example dataset

Gene expression data (*.txt)

REMBRANDT_ODII_AII_log2_normalized_data.txt

We have downloaded raw CEL files from 65 astrocytoma grade II and 30 oligodendroglioma grade II microarrays at the REMBRANDT portal ( https://caintegrator.nci.nih.gov/rembrandt), and then used the justRMA function from the affy package ( http://www.bioconductor.org/packages/release/bioc/html/affy.html) to pre-process them. To group probes into probe sets, we have used the Brain array custom CDF file (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), ENTREZG v. 18.0.0.0.

Annotation data (*.chip)

No annotation data is required in this example. If you need to collapse your dataset to gene symbols, you can download CHIP files from the Broad ftp site (ftp://gseaftp.broadinstitute.org/pub/gsea/annotations).

Phenotype data (*.cls)

REMBRANDT_AII_ODII.cls

In this file, "AII" means astrocytoma grade II, and "ODII" means oligodendroglioma grade II.

Collection of gene sets (*.gmt)

Before running CoGA, you must enter a collection of gene sets.

You can find several collections of gene sets in gmt format freely available at the Molecular Signature Database (MSigDB) (http://www.broadinstitute.org/gsea/msigdb/collections.jsp).