sagenhaft

DOI: 10.18129/B9.bioc.sagenhaft  

Collection of functions for reading and comparing SAGE libraries

Bioconductor version: Release (3.17)

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 "4.3") 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")

 

PDF	R Script	SAGEnhaft
PDF		Reference Manual

Details

biocViews	SAGE, Software
Version	1.70.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18.5 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_1.70.0.tar.gz
Windows Binary	sagenhaft_1.70.0.zip (64-bit only)
macOS Binary (x86_64)	sagenhaft_1.70.0.tgz
macOS Binary (arm64)	sagenhaft_1.70.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sagenhaft
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sagenhaft
Bioc Package Browser	https://code.bioconductor.org/browse/sagenhaft/
Package Short Url	https://bioconductor.org/packages/sagenhaft/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive