sagenhaft

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Collection of functions for reading and comparing SAGE libraries

Bioconductor version: Development (3.24)

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")):

Tim Beissbarth, with contributions from Gordon Smyth. sagenhaft: Collection of functions for reading and comparing SAGE libraries. doi:10.18129/B9.bioc.sagenhaft, R package version 1.83.0, https://bioconductor.org/packages/sagenhaft.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

SAGEnhaft	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	SAGE, Software
Version	1.83.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 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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Build Report	Build Report, r-universe

Package Archives

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

Source Package	sagenhaft_1.83.0.tar.gz
Windows Binary (x86_64)	sagenhaft_1.83.0.zip
macOS Binary (big-sur-x86_64)	sagenhaft_1.83.0.tgz
macOS Binary (sonoma-arm64)	sagenhaft_1.83.0.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