sagenhaft

DOI: 10.18129/B9.bioc.sagenhaft    

Collection of functions for reading and comparing SAGE libraries

Bioconductor version: Release (3.13)

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 bioinf.med.uni-goettingen.de>, with contributions from Gordon Smyth <smyth at wehi.edu.au>

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

Installation

To install this package, start R (version "4.1") 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	1.62.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 16.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10), SparseM (>= 0.73), methods
Imports	graphics, stats, utils
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URL	http://www.bioinf.med.uni-goettingen.de
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Build Report

Package Archives

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

Source Package	sagenhaft_1.62.0.tar.gz
Windows Binary	sagenhaft_1.62.0.zip
macOS 10.13 (High Sierra)	sagenhaft_1.62.0.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