Tang Lab In the Department of Genetics

SABER

Beta version of SABER+. You need java and R installed. Please let us know if you have any problems running the program, or if you have ideas to make the program more user-friendly!

This is the first version of SABER. The package is written in R, and was tested under a Linux system. It has not been thoroughly tested under other systems.

Download the package

We are still looking for a “permanent home” for SABER.
For now, you can download the package here (590KB).

Hardware and software pre-requisites

It is assumed that R 2.4.0 or later has been installed on your machine. R is a free software, and can be downloaded from the R website. SABER requires access to lapack complex routines beyond those supplied by R; see the configure.in file for hints. Package functionality requires R >= 2.2.0, but the sample data and examples assume R >= 2.4.0.

Installation

To installSABER, run command line (from the parent directory):

R CMD INSTALL SABER

On Mac OSX, you need XCode 2.4 or newer.
On some UNIX machines, you may want to try

R CMD INSTALL --configure-args=--with-lapack=/usr/lib/liblapack.so SABER

Tutorial

A tutorial for basic functionalities is provided via a vignette in R. A pdf of the tutorial is in "HowTo.pdf." After you have installed SABER, start R, and type the following lines to get started:

library(help=SABER)
library(SABER) #load the library
vignette(“HowTo”) #view the vignette
? Genome # see the genome help page
example(Genome) #run the examples at the bottom of the ‘Genome’ help page

Comments and Feedback

Thank you for using SABER. Good luck, and please let us know if you have trouble installing or using the program. Please email us at Hua Tang (huatang at stanford dot edu) and Martin Morgan (mtmorgan at fhcrc dot org).

 

 

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