sagenhaft: Collection of functions for reading and comparing SAGE libraries

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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@ams.med.uni-goettingen.de>, with contributions from Gordon Smyth <smyth@wehi.edu.au> and Lavinia Hyde <hyde@wehi.edu.au>.
Date of publication
None
Maintainer
Tim Beissbarth <tim.beissbarth@ams.med.uni-goettingen.de>
License
GPL (>= 2)
Version
1.44.0
URLs

View on Bioconductor

Man pages

error.correction
Estimate sequencing errors and compute corrected counts
extract.lib
Functions for SAGE library extraction
sage.library
Class sage.library
sage.library.comparison
Class sage.library.comparison
sagelibrary.simulate
Simulate SAGE libraries
sage.test
Compare Two SAGE Libraries
sage.utilities
Utilities

Files in this package

sagenhaft/DESCRIPTION
sagenhaft/NAMESPACE
sagenhaft/R
sagenhaft/R/sagenhaft.R
sagenhaft/build
sagenhaft/build/vignette.rds
sagenhaft/data
sagenhaft/data/SAGEartifacts.txt.gz
sagenhaft/inst
sagenhaft/inst/doc
sagenhaft/inst/doc/SAGEnhaft.R
sagenhaft/inst/doc/SAGEnhaft.Rnw
sagenhaft/inst/doc/SAGEnhaft.pdf
sagenhaft/inst/extdata
sagenhaft/inst/extdata/B6HypothalHFI.sage
sagenhaft/inst/extdata/E15postHFI.sage
sagenhaft/inst/extdata/E15postHFI.zip
sagenhaft/man
sagenhaft/man/error.correction.Rd
sagenhaft/man/extract.lib.Rd
sagenhaft/man/sage.library.Rd
sagenhaft/man/sage.library.comparison.Rd
sagenhaft/man/sage.test.Rd
sagenhaft/man/sage.utilities.Rd
sagenhaft/man/sagelibrary.simulate.Rd
sagenhaft/vignettes
sagenhaft/vignettes/SAGEnhaft.Rnw