sagenhaft

DOI: 10.18129/B9.bioc.sagenhaft    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see sagenhaft.

Collection of functions for reading and comparing SAGE libraries

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	SAGEnhaft
PDF		Reference Manual

Details

biocViews	SAGE, Software
Version	1.54.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10), SparseM (>= 0.73), methods
Imports	graphics, methods, SparseM, stats, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://tagcalling.mbgproject.org
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	sagenhaft_1.54.0.tar.gz
Windows Binary	sagenhaft_1.54.0.zip
Mac OS X 10.11 (El Capitan)	sagenhaft_1.54.0.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