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sagenhaft

Collection of functions for reading and comparing SAGE libraries


Bioconductor version: Release (3.18)

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>

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

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")
SAGEnhaft PDF R Script
Reference Manual PDF

Details

biocViews SAGE, Software
Version 1.72.0
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, stats, utils
System Requirements
URL http://www.bioinf.med.uni-goettingen.de
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Package Archives

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

Source Package sagenhaft_1.72.0.tar.gz
Windows Binary sagenhaft_1.72.0.zip
macOS Binary (x86_64) sagenhaft_1.72.0.tgz
macOS Binary (arm64) sagenhaft_1.72.0.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/
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