Tools for visualizing genomics data
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.
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.
Detailed usage examples are available in the Vignette.
- 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
- Doug Phanstiel
- Alan Boyle
- Caros Araya
The code is freely available under the GPL (>= 2) license