sagenhaft: Collection of functions for reading and comparing SAGE libraries

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sagenhaft")
AuthorTim Beissbarth <tim.beissbarth@ams.med.uni-goettingen.de>, with contributions from Gordon Smyth <smyth@wehi.edu.au> and Lavinia Hyde <hyde@wehi.edu.au>.
Bioconductor views SAGE
Date of publicationNone
MaintainerTim Beissbarth <tim.beissbarth@ams.med.uni-goettingen.de>
LicenseGPL (>= 2)
Version1.46.0
http://tagcalling.mbgproject.org

View on Bioconductor

Functions

combine.libs Man page
compare.lib.pair Man page
compute.sequence.neighbors Man page
compute.unique.tags Man page
create.matrix.csr Man page
difference.scatter.plot Man page
em.estimate.error.given Man page
estimate.errors.mean Man page
extract.ditags Man page
extract.lib.from.directory Man page
extract.lib.from.zip Man page
extract.library.tags Man page
plot.sage.library Man page
plot.sage.library.comparison Man page
print.sage.library Man page
print.sage.library.comparison Man page
read.phd.file Man page
read.sage.library Man page
read.sage.library.comparison Man page
read.seq.qual.filepair Man page
reestimate.lib.from.tagcounts Man page
remove.sage.artifacts Man page
revcomp Man page
SAGEartifacts Man page
sagelibrary.simulate Man page
sage.test Man page
summary.sage.library Man page
summary.sage.library.comparison Man page
table.sparse Man page
tagmatrix2tagnum Man page
tagnum2tagmatrix Man page
tagnum2tagsequence Man page
tagsequence2tagnum Man page
write.sage.library Man page
write.sage.library.comparison Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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