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

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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.

Author
Sylvain Gubian <DL.RSupport@pmi.com>, Alain Sewer <DL.RSupport@pmi.com>, PMP SA
Date of publication
None
Maintainer
Sylvain Gubian <DL.RSupport@pmi.com>
License
GPL-2
Version
2.16.0

View on Bioconductor

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.

Files in this package

ExiMiR/DESCRIPTION
ExiMiR/LICENSE
ExiMiR/NAMESPACE
ExiMiR/NEWS
ExiMiR/R
ExiMiR/R/NormiR.R
ExiMiR/R/NormiR.methods.R
ExiMiR/R/createAB.R
ExiMiR/R/make.gal.env.R
ExiMiR/R/read.exi.R
ExiMiR/build
ExiMiR/build/vignette.rds
ExiMiR/data
ExiMiR/data/GSE19183.rda
ExiMiR/data/GSE20122.rda
ExiMiR/data/galenv.rda
ExiMiR/inst
ExiMiR/inst/doc
ExiMiR/inst/doc/ExiMiR-vignette.R
ExiMiR/inst/doc/ExiMiR-vignette.Rnw
ExiMiR/inst/doc/ExiMiR-vignette.pdf
ExiMiR/man
ExiMiR/man/ExiMiR-package.Rd
ExiMiR/man/GSE19183.Rd
ExiMiR/man/GSE20122.Rd
ExiMiR/man/NormiR.Rd
ExiMiR/man/NormiR.methods.Rd
ExiMiR/man/ReadExi.Rd
ExiMiR/man/bg.correct.miR.Rd
ExiMiR/man/createAB.Rd
ExiMiR/man/galenv.Rd
ExiMiR/man/make.gal.env.Rd
ExiMiR/man/norm.miR.Rd
ExiMiR/man/summarize.miR.Rd
ExiMiR/vignettes
ExiMiR/vignettes/ExiMiR-vignette.Rnw
ExiMiR/vignettes/fig0.png
ExiMiR/vignettes/fig1.png
ExiMiR/vignettes/fig2.png
ExiMiR/vignettes/fig3.png
ExiMiR/vignettes/samplesinfo.txt