sagenhaft

DOI: 10.18129/B9.bioc.sagenhaft    

This is the development version of sagenhaft; for the stable release version, see sagenhaft.

Collection of functions for reading and comparing SAGE libraries

Bioconductor version: Development (3.11)

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 "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.57.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 15 years)
License GPL (>= 2)
Depends R (>= 2.10), SparseM (>= 0.73), methods
Imports graphics, stats, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL http://www.bioinf.med.uni-goettingen.de
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_1.57.0.tar.gz
Windows Binary sagenhaft_1.57.0.zip
Mac OS X 10.11 (El Capitan)
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: