Bioconductor-mirror/HELP: Tools for HELP data analysis

The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.

Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("Bioconductor-mirror/HELP")
AuthorReid F. Thompson <reid.thompson@gmail.com>, John M. Greally <john.greally@einstein.yu.edu>, with contributions from Mark Reimers <mreimers@vcu.edu>
Date of publicationNone
MaintainerReid F. Thompson <reid.thompson@gmail.com>
LicenseGPL (>= 2)
Version1.35.0

View on GitHub

Functions

base.stacking.thermodynamics Man page
calcGC Man page
calcGC,character-method Man page
calcGC,ExpressionSet-method Man page
calcGC-methods Man page
calcGC,missing-method Man page
calcGC,NULL-method Man page
calcPrototype Man page
calcPrototype,ExpressionSet-method Man page
calcPrototype,matrix-method Man page
calcPrototype-methods Man page
calcPrototype,missing-method Man page
calcPrototype,vector-method Man page
calcTm Man page
calcTm,character-method Man page
calcTm,ExpressionSet-method Man page
calcTm-methods Man page
calcTm,missing-method Man page
calcTm,NULL-method Man page
combineData Man page
combineData,ExpressionSet,missing,missing-method Man page
combineData,ExpressionSet,vector,missing-method Man page
combineData,matrix,vector,matrix-method Man page
combineData,matrix,vector,missing-method Man page
combineData-methods Man page
combineData,missing,missing,missing-method Man page
combineData,vector,missing,missing-method Man page
combineData,vector,missing,vector-method Man page
combineData,vector,vector,missing-method Man page
combineData,vector,vector,vector-method Man page
createWiggle Man page
createWiggle,ExpressionSet,matrix-method Man page
createWiggle,ExpressionSet,missing-method Man page
createWiggle,matrix,matrix-method Man page
createWiggle-methods Man page
createWiggle,missing,missing-method Man page
createWiggle,vector,matrix-method Man page
exprs2 Man page
exprs2<- Man page
exprs2<-,ExpressionSet,matrix-method Man page
exprs2,ExpressionSet-method Man page
exprs2<-,ExpressionSet,missing-method Man page
exprs2-methods Man page
exprs2,missing-method Man page
fuzzyMatches Man page
fuzzyMatches-methods Man page
fuzzyMatches,missing,missing-method Man page
fuzzyMatches,NULL,vector-method Man page
fuzzyMatches,vector,missing-method Man page
fuzzyMatches,vector,NULL-method Man page
fuzzyMatches,vector,vector-method Man page
getFeatures Man page
getFeatures,AnnotatedDataFrame,missing-method Man page
getFeatures,AnnotatedDataFrame,NULL-method Man page
getFeatures,AnnotatedDataFrame,vector-method Man page
getFeatures,ExpressionSet,missing-method Man page
getFeatures,ExpressionSet,NULL-method Man page
getFeatures,ExpressionSet,vector-method Man page
getFeatures,matrix,vector-method Man page
getFeatures-methods Man page
getFeatures,missing,missing-method Man page
getFeatures,vector,missing-method Man page
getFeatures,vector,NULL-method Man page
getFeatures,vector,vector-method Man page
getSamples Man page
getSamples,ExpressionSet,missing-method Man page
getSamples,ExpressionSet,NULL-method Man page
getSamples,ExpressionSet,vector-method Man page
getSamples,matrix,missing-method Man page
getSamples,matrix,NULL-method Man page
getSamples,matrix,vector-method Man page
getSamples-methods Man page
getSamples,missing,missing-method Man page
getSamples,vector,missing-method Man page
getSamples,vector,NULL-method Man page
getSamples,vector,vector-method Man page
plotBins Man page
plotBins,ExpressionSet,ExpressionSet-method Man page
plotBins,ExpressionSet,missing-method Man page
plotBins,ExpressionSet,vector-method Man page
plotBins,matrix,missing-method Man page
plotBins-methods Man page
plotBins,missing,missing-method Man page
plotBins,vector,ExpressionSet-method Man page
plotBins,vector,missing-method Man page
plotBins,vector,vector-method Man page
plotChip Man page
plotChip,ExpressionSet,ExpressionSet,missing-method Man page
plotChip,ExpressionSet,missing,missing-method Man page
plotChip,ExpressionSet,vector,missing-method Man page
plotChip,matrix,missing,missing-method Man page
plotChip-methods Man page
plotChip,missing,missing,missing-method Man page
plotChip,vector,vector,ExpressionSet-method Man page
plotChip,vector,vector,vector-method Man page
plotFeature Man page
plotFeature,ExpressionSet,missing-method Man page
plotFeature,ExpressionSet,vector-method Man page
plotFeature,matrix,vector-method Man page
plotFeature-methods Man page
plotFeature,missing,missing-method Man page
plotPairs Man page
plotPairs,ExpressionSet-method Man page
plotPairs,matrix-method Man page
plotPairs-methods Man page
plotPairs,missing-method Man page
quantileNormalize Man page
quantileNormalize,ExpressionSet,ExpressionSet-method Man page
quantileNormalize,ExpressionSet,missing-method Man page
quantileNormalize,ExpressionSet,vector-method Man page
quantileNormalize,matrix,missing-method Man page
quantileNormalize-methods Man page
quantileNormalize,missing,missing-method Man page
quantileNormalize,vector,ExpressionSet-method Man page
quantileNormalize,vector,missing-method Man page
quantileNormalize,vector,vector-method Man page
readDesign Man page
readDesign,character,character,character-method Man page
readDesign,character,character,ExpressionSet-method Man page
readDesign-methods Man page
readDesign,missing,missing,missing-method Man page
readDesign,vector,missing,missing-method Man page
readDesign,vector,vector,missing-method Man page
readPairs Man page
readPairs,character,character,character-method Man page
readPairs,character,character,ExpressionSet-method Man page
readPairs-methods Man page
readPairs,missing,missing,missing-method Man page
readPairs,vector,missing,missing-method Man page
readPairs,vector,vector,missing-method Man page
readSampleKey Man page

Files

DESCRIPTION
NAMESPACE
R/calcGC.R R/calcPrototype.R R/calcTm.R R/combineData.R R/createWiggle.R R/exprs2.R R/fuzzyMatches.R R/getFeatures.R R/getSamples.R R/plotBins.R R/plotChip.R R/plotFeature.R R/plotPairs.R R/quantileNormalize.R R/readDesign.R R/readPairs.R R/readSampleKey.R
data/base.stacking.thermodynamics.RData
demo/00Index
demo/pipeline.R
inst/pipeline.data/70989_532.pair.txt
inst/pipeline.data/70989_635.pair.txt
inst/pipeline.data/71083_532.pair.txt
inst/pipeline.data/71083_635.pair.txt
inst/pipeline.data/71420_532.pair.txt
inst/pipeline.data/71420_635.pair.txt
inst/pipeline.data/HELP.ndf.txt
inst/pipeline.data/HELP.ngd.txt
inst/pipeline.data/HELP.pos.txt
inst/pipeline.data/sample.key.txt
man/base.stacking.thermodynamics.Rd man/calcGC-methods.Rd man/calcGC.Rd man/calcPrototype-methods.Rd man/calcPrototype.Rd man/calcTm-methods.Rd man/calcTm.Rd man/combineData-methods.Rd man/combineData.Rd man/createWiggle-methods.Rd man/createWiggle.Rd man/exprs2-methods.Rd man/exprs2.Rd man/fuzzyMatches-methods.Rd man/fuzzyMatches.Rd man/getFeatures-methods.Rd man/getFeatures.Rd man/getSamples-methods.Rd man/getSamples.Rd man/plotBins-methods.Rd man/plotBins.Rd man/plotChip-methods.Rd man/plotChip.Rd man/plotFeature-methods.Rd man/plotFeature.Rd man/plotPairs-methods.Rd man/plotPairs.Rd man/quantileNormalize-methods.Rd man/quantileNormalize.Rd man/readDesign-methods.Rd man/readDesign.Rd man/readPairs-methods.Rd man/readPairs.Rd man/readSampleKey.Rd
vignettes/HELP.Rnw
vignettes/HELP.bib

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

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

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