AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips
Version 2.26.0

Processing and Analysis of Agilent microRNA data

AuthorPedro Lopez-Romero <plopez@cnic.es>
Bioconductor views AgilentChip DifferentialExpression Microarray OneChannel Preprocessing
Date of publicationNone
MaintainerPedro Lopez-Romero <plopez@cnic.es>
LicenseGPL-3
Version2.26.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AgiMicroRna")

Popular man pages

dd.micro: data example (uRNAList)
mvaBASIC: MVA plot
qcPlots: Plots for Quality Assessment
readMicroRnaAFE: Read Agilent Feature Extraction txt data files
RleMicroRna: Relative Log Expression
targets.micro: Example of target file
uRNAList: uRNAList - class
See all...

All man pages Function index File listing

Man pages

basicLimma: Linear models Using limma
boxplotMicroRna: Boxplot
cvArray: Coefficient of variation of replicated probes within array
dd.micro: data example (uRNAList)
ddPROC: Processed miRNA data (uRNAList)
dimnames.uRNAList: Retrieve the Dimension Names of an uRNAList Object
dim.uRNAList: Retrieve the Dimensions of an uRNAList Object
esetMicroRna: ExpressionSet object from a uRNAList
filterMicroRna: Filtering Genes
getDecideTests: Differential expression analysis an multiplicity of the tests
HeatMapMicroRna: HeatMap
hierclusMicroRna: Hierarchical clustering
mvaBASIC: MVA plot
mvaMicroRna: MA plot
PCAplotMicroRna: PCA plot
plotDensityMicroRna: Density Plots of Intensity Signals
pvalHistogram: Histogram of the p values
qcPlots: Plots for Quality Assessment
readMicroRnaAFE: Read Agilent Feature Extraction txt data files
readTargets: read the target file
RleMicroRna: Relative Log Expression
rmaMicroRna: Getting the Total Gene Signal by RMA algorithm
significantMicroRna: Summarize Differential Expression Results
summary.uRNAList: Summaries of Microarray Data Objects
targets.micro: Example of target file
tgsMicroRna: Getting the Total Gene Signal
tgsNormalization: Normalization Between Arrays
uRNAList: uRNAList - class
writeEset: Writes the expression data matrix of an ExpressionSet object...

Functions

HeatMapMicroRna Man page
PCAplotMicroRna Man page
RleMicroRna Man page
basicLimma Man page
boxplotMicroRna Man page
cvArray Man page
dd.micro Man page
ddPROC Man page
dim.uRNAList Man page Source code
dimnames.uRNAList Man page Source code
dimnames<-.uRNAList Man page
esetMicroRna Man page
filterMicroRna Man page
getDecideTests Man page
hierclusMicroRna Man page
length.uRNAList Man page Source code
mvaBASIC Man page
mvaMicroRna Man page
plotDensityMicroRna Man page
printHead Source code
pvalHistogram Man page
qcPlots Man page
readMicroRnaAFE Man page
readTargets Man page
rmaMicroRna Man page
setdimnames Source code
show,uRNAList-method Man page
significantMicroRna Man page
summary.uRNAList Man page Source code
targets.micro Man page
tgsMicroRna Man page
tgsNormalization Man page
uRNAList-class Man page
writeEset Man page

Files

DESCRIPTION
NAMESPACE
R
R/AgiMicroRNA-classes.R
R/DEG.print.info.R
R/HeatMapMicroRna.R
R/MA.plot.miRNA.R
R/PCAplotMicroRna.R
R/RleMicroRna.R
R/basicLimma.R
R/boxplotMicroRna.R
R/cv.array.R
R/cvArray.R
R/esetMicroRna.R
R/filter.IsGeneDetected.R
R/filter.control.miRNA.R
R/filter.wellaboveNEG.miRNA.R
R/filterFLAG.micro.R
R/filterMicroRna.R
R/filterWellAboveSIGNALv2.R
R/getDecideTests.R
R/getTDRows2.R
R/hierclusMicroRna.R
R/miRNA.htmlpage.R
R/mvaBASIC.R
R/mvaMicroRna.R
R/paste.character.R
R/plotDensityMicroRna.R
R/pvalHistogram.R
R/qcPlots.R
R/read.agiMicroRna.R
R/readMicroRnaAFE.R
R/readTargets.R
R/rmaMicroRna.R
R/significantMicroRna.R
R/subsetting.R
R/tgsMicroRna.R
R/tgsNormalization.R
R/write.LIST.miRNA.R
R/write.control.out.miRNA.R
R/write.filt.out.miRNA.R
R/writeEset.R
build
build/vignette.rds
data
data/datalist
data/dd.micro.rda
data/ddPROC.rda
data/targets.micro.rda
inst
inst/doc
inst/doc/AgiMicroRna.R
inst/doc/AgiMicroRna.Rnw
inst/doc/AgiMicroRna.pdf
man
man/HeatMapMicroRna.Rd
man/PCAplotMicroRna.Rd
man/RleMicroRna.Rd
man/basicLimma.Rd
man/boxplotMicroRna.Rd
man/cvArray.Rd
man/dd.micro.Rd
man/ddPROC.Rd
man/dim.uRNAList.Rd
man/dimnames.uRNAList.Rd
man/esetMicroRna.Rd
man/filterMicroRna.Rd
man/getDecideTests.Rd
man/hierclusMicroRna.Rd
man/mvaBASIC.Rd
man/mvaMicroRna.Rd
man/plotDensityMicroRna.Rd
man/pvalHistogram.Rd
man/qcPlots.Rd
man/readMicroRnaAFE.Rd
man/readTargets.Rd
man/rmaMicroRna.Rd
man/significantMicroRna.Rd
man/summary.uRNAList.Rd
man/targets.micro.Rd
man/tgsMicroRna.Rd
man/tgsNormalization.Rd
man/uRNAList.Rd
man/writeEset.Rd
vignettes
vignettes/AgiMicroRna.Rnw
vignettes/AgiMicroRna.bib
AgiMicroRna documentation built on May 20, 2017, 10:59 p.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.