ExiMiR: R functions for the normalization of Exiqon miRNA array data
Version 2.18.0

This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.

AuthorSylvain Gubian <DL.RSupport@pmi.com>, Alain Sewer <DL.RSupport@pmi.com>, PMP SA
Bioconductor views GeneExpression Microarray OneChannel Preprocessing Transcription TwoChannel
Date of publicationNone
MaintainerSylvain Gubian <DL.RSupport@pmi.com>
LicenseGPL-2
Version2.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ExiMiR")

Getting started

Package overview

Popular man pages

bg.correct.miR: ExiMiR low-level function for background correction
ExiMiR-package: R functions for the normalization of Exiqon miRNA array data
GSE19183: Affybatch object for the raw data from GEO series GSE19183
NormiR: ExiMiR high-level function for miRNA raw data normalization.
NormiR.methods: ExiMiR functions for enumerating the names of low-level...
ReadExi: ExiMiR function for reading Exiqon raw data into an AffyBatch...
summarize.miR: ExiMiR low-level function for summarization.
See all...

All man pages Function index File listing

Man pages

bg.correct.miR: ExiMiR low-level function for background correction
createAB: ExiMiR function for creating an AffyBatch object from other...
ExiMiR-package: R functions for the normalization of Exiqon miRNA array data
galenv: R annotation environment for GEO series GSE20122
GSE19183: Affybatch object for the raw data from GEO series GSE19183
GSE20122: Affybatch object for the raw data from GEO series GSE20122
make.gal.env: GAL Environment Maker
NormiR: ExiMiR high-level function for miRNA raw data normalization.
NormiR.methods: ExiMiR functions for enumerating the names of low-level...
norm.miR: ExiMiR low-level function for miRNA raw data normalization.
ReadExi: ExiMiR function for reading Exiqon raw data into an AffyBatch...
summarize.miR: ExiMiR low-level function for summarization.

Functions

ExiMiR Man page
GSE19183 Man page
GSE20122 Man page
NormiR Man page Source code
NormiR.bgcorrect.methods Man page Source code
NormiR.normalize.methods Man page Source code
NormiR.pmcorrect.methods Man page Source code
NormiR.spikein.args Man page Source code
NormiR.summary.methods Man page Source code
ReadExi Man page Source code
bcr2i Source code
bg.boxplot Source code
bg.correct.miR Man page Source code
bg.hist Source code
bg.image Source code
by.samples.curve Source code
by.samples.figures Source code
by.samples.legend Source code
create.gal.env Source code
createAB Man page Source code
galenv Man page
get.bg.ab Source code
has.bg Source code
i2bcr Source code
is.dual Source code
is.from.createAB Source code
make.gal.env Man page Source code
meannorm Source code
mediannorm Source code
norm.miR Man page Source code
read.annotation.fromfile Source code
spikeinnorm Source code
summarize.miR Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/NormiR.R
R/NormiR.methods.R
R/createAB.R
R/make.gal.env.R
R/read.exi.R
build
build/vignette.rds
data
data/GSE19183.rda
data/GSE20122.rda
data/galenv.rda
inst
inst/doc
inst/doc/ExiMiR-vignette.R
inst/doc/ExiMiR-vignette.Rnw
inst/doc/ExiMiR-vignette.pdf
man
man/ExiMiR-package.Rd
man/GSE19183.Rd
man/GSE20122.Rd
man/NormiR.Rd
man/NormiR.methods.Rd
man/ReadExi.Rd
man/bg.correct.miR.Rd
man/createAB.Rd
man/galenv.Rd
man/make.gal.env.Rd
man/norm.miR.Rd
man/summarize.miR.Rd
vignettes
vignettes/ExiMiR-vignette.Rnw
vignettes/fig0.png
vignettes/fig1.png
vignettes/fig2.png
vignettes/fig3.png
vignettes/samplesinfo.txt
ExiMiR documentation built on May 20, 2017, 10:07 p.m.

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