SABER (Version 1.0)

Hua Tang (huatang at stanford dot edu) and Martin Morgan (mtmorgan at fhcrc dot org)

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 should check here often for update.

 

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 install SABER, 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. 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

 

A pdf of the tutorial is in HowTo.pdf.

 

Comments and Feedback

Thank you for using SABER. Good luck, and please let us know if you have trouble installing or using the program.