To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("sagenhaft")

In most cases, you don't need to download the package archive at all.

sagenhaft

Collection of functions for reading and comparing SAGE libraries

Bioconductor version: Release (3.0)

This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.

Author: Tim Beissbarth <beissbarth at wehi.edu.au>, with contributions from Gordon Smyth <smyth at wehi.edu.au> and Lavinia Hyde <hyde at wehi.edu.au>.

Maintainer: Tim Beissbarth <beissbarth at wehi.edu.au>

Citation (from within R, enter citation("sagenhaft")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("sagenhaft")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sagenhaft")

 

PDF R Script SAGEnhaft
PDF   Reference Manual

Details

biocViews SAGE, Software
Version 1.36.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License GPL (>= 2)
Depends R (>= 2.10), SparseM (>= 0.73), methods
Imports graphics, methods, SparseM, stats, utils
Suggests
System Requirements
URL http://tagcalling.mbgproject.org
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source sagenhaft_1.36.0.tar.gz
Windows Binary sagenhaft_1.36.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) sagenhaft_1.36.0.tgz
Mac OS X 10.9 (Mavericks) sagenhaft_1.36.0.tgz
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