This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

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>

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 1.70.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License GPL (>= 2)
Depends R (>= 2.10), SparseM (>= 0.73), methods
Imports graphics, stats, utils
Linking To
Suggests
System Requirements
Enhances
URL http://www.bioinf.med.uni-goettingen.de
See More
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_1.70.0.tar.gz
Windows Binary sagenhaft_1.70.0.zip
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