Sushi

Tools for visualizing genomics data

Deprecation Notice

This package has been deprecated and will no longer be maintained. For an actively maintained genomic data visualization package, please take a look at plotgardener.

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

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("PhanstielLab/Sushi")

Install release version 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.
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
```
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

License

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

PhanstielLab / Sushi