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Welcome

Welcome to CAFE! =D

NEWS

For news, click here

INSTALLATION

How to install CAFE depends on your operating system. System requirements are R 2.10 or up, although we recommend using the newest version of R, which is currently 3.0.1. Furthermore we recommend having adequate memory available, with 4 GB RAM being a workable minimum. It is advisable to have some kind of SWAP memory available, especially if you use the computer for other purposes as well.

Linux

If you use a Linux machine, you can simply download the CAFE_x.x.x.x.tar.gz file. If you already have all dependencies - likely if you're an avid BioConductor user - you can simply type the following in a terminal:

$ R CMD INSTALL /path/to/CAFE/download

Debian-based systems

For Debian-based systems - Ubuntu, Linux Mint, Crunchbang etc - we provide an install script that automatically installs all dependencies. Download CAFE_install_debain1.0.tar.gz, untar it, modify cafeInstall.sh on line 11 to correct the path to where you downloaded CAFE, and run this same script afterwards.

Non-debian users can also run the dependencies.R script to install all R dependencies, although this might exclude some CURL and XML packages that have to be installed on your system before.

Windows

For windows, you can download the CAFE_x.x.x.x_WINDOWS.rar file. This contains 4 different CAFE builds, build for R 2.15 and R 3.0, with both the i386 and x86_64 architectures. Unpack the file, and install the correct build of CAFE for your system in RGui by: packages --> install packages from local zip file(s) --> select the correct build. Before you can install CAFE, all dependencies (see below) must already have been installed. You can install these by doing the following in RGui packages --> install packages.

Dependencies

The list of R dependencies is currently: biovizBase, GenomicRanges, IRanges, ggbio, affy, ggplot2, reshape2, annotate, grid, gridExtra, tcltk and Biobase

Vignettte

To see the package vignette, click here

Cite

An article describing CAFE is now in press in Bioinformatics.

Please cite the following if you have used CAFE:

Bollen, S., M. Leddin, M.A. Andrade-Navarro and N. Mah. 2014. CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. Bioinformatics. In press.

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