Sushi

Tools for visualizing genomics data

Citation

Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinformatics. 2014 Oct;30(19):2808-10.

Features

Detailed usage examples are available in the Vignette.

Sushi Installation

1. To install the latest version directly from github open R and run the following commands (requires the R package devtools which is available through CRAN):

library("devtools")
install_github("dphansti/Sushi")

2. Install release verson with Bioconductor:

source("http://bioconductor.org/biocLite.R")
biocLite("Sushi")

Note: R 3.1 is required for installation via Bioconductor. The newest version of R can be downloaded at (www.r-project.org/). Installation via Bioconductor also requires libcurl and libxml2 which may not be be standard with some Linux distributions and are available for download at (http://curl.haxx.se/libcurl/ and http://xmlsoft.org/, respectively.

3. Install from source (for previous versions of R >= 2.10):

Download source code from http://www.bioconductor.org/packages/release/bioc/html/Sushi.html

R CMD INSTALL Sushi_X.X.X.tar.gz

4. The development version of Sushi can be downloaded via Bioconductor

source("http://bioconductor.org/biocLite.R")
useDevel()
biocLite("Sushi")

or via source at http://www.bioconductor.org/packages/devel/bioc/html/Sushi.html

Contributors

• Doug Phanstiel
• Alan Boyle
• Caros Araya

License

The code is freely available under the GPL (>= 2) license