HELP: Tools for HELP data analysis
Version 1.34.0

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

Browse man pages Browse package API and functions Browse package files

AuthorReid F. Thompson <reid.thompson@gmail.com>, John M. Greally <john.greally@einstein.yu.edu>, with contributions from Mark Reimers <mreimers@vcu.edu>
Bioconductor views CpGIsland DNAMethylation DataImport Microarray Preprocessing QualityControl TwoChannel Visualization
Date of publicationNone
MaintainerReid F. Thompson <reid.thompson@gmail.com>
LicenseGPL (>= 2)
Version1.34.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HELP")

Man pages

base.stacking.thermodynamics: Base-stacking thermodynamic parameters
calcGC: Calculate GC percent
calcGC-methods: Calculate GC percent (methods)
calcPrototype: Calculate prototype
calcPrototype-methods: Calculate prototype (methods)
calcTm: Calculate Tm
calcTm-methods: Calculate Tm (methods)
combineData: Combine data
combineData-methods: Combine data (methods)
createWiggle: Create wiggle track
createWiggle-methods: Create wiggle track (methods)
exprs2: Retrieve microarray data (for signal channel 2) from...
exprs2-methods: Retrieve microarray data (for signal channel 2) from...
fuzzyMatches: Fuzzy matching
fuzzyMatches-methods: Fuzzy matching (methods)
getFeatures: Get features (methods)
getFeatures-methods: Get features (methods)
getSamples: Get samples
getSamples-methods: Get samples (methods)
plotBins: Plot bins
plotBins-methods: Plot bins (methods)
plotChip: Plot chip image
plotChip-methods: Plot chip image (methods)
plotFeature: Plot feature versus two-color intensity
plotFeature-methods: Plot feature versus two-color intensity (methods)
plotPairs: Plot tree-pairs
plotPairs-methods: Plot tree-pairs (methods)
quantileNormalize: Quantile normalization
quantileNormalize-methods: Quantile normalization (methods)
readDesign: Read NimbleGen design files
readDesign-methods: Read NimbleGen design files (methods)
readPairs: Read Nimblegen .pair files
readPairs-methods: Read Nimblegen .pair files (methods)
readSampleKey: Read sample key

Functions

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

Files

DESCRIPTION
NAMESPACE
R
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
build
build/vignette.rds
data
data/base.stacking.thermodynamics.RData
demo
demo/00Index
demo/pipeline.R
inst
inst/doc
inst/doc/HELP.R
inst/doc/HELP.Rnw
inst/doc/HELP.pdf
inst/pipeline.data
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
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
vignettes/HELP.Rnw
vignettes/HELP.bib
HELP documentation built on May 20, 2017, 9:48 p.m.