README.md

In dphansti/Sushi: Tools for visualizing genomics data

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

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("PhanstielLab/Sushi")

1. 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.

1. 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

1. 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

dphansti/Sushi documentation built on Oct. 30, 2021, 10:20 p.m.