sagenhaft

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see sagenhaft.

Collection of functions for reading and comparing SAGE libraries


Bioconductor version: 3.7

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 <tim.beissbarth at ams.med.uni-goettingen.de>, with contributions from Gordon Smyth <smyth at wehi.edu.au> and Lavinia Hyde <hyde at wehi.edu.au>.

Maintainer: Tim Beissbarth <tim.beissbarth at ams.med.uni-goettingen.de>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sagenhaft")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("sagenhaft")
SAGEnhaft PDF R Script
Reference Manual PDF

Details

biocViews SAGE, Software
Version 1.50.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License GPL (>= 2)
Depends R (>= 2.10), SparseM (>= 0.73), methods
Imports graphics, methods, SparseM, stats, utils
System Requirements
URL http://tagcalling.mbgproject.org
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Package Archives

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

Source Package sagenhaft_1.50.0.tar.gz
Windows Binary sagenhaft_1.50.0.zip
Mac OS X 10.11 (El Capitan) sagenhaft_1.50.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sagenhaft
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sagenhaft
Package Short Url https://bioconductor.org/packages/sagenhaft/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive