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.

Author
Reid F. Thompson <reid.thompson@gmail.com>, John M. Greally <john.greally@einstein.yu.edu>, with contributions from Mark Reimers <mreimers@vcu.edu>
Date of publication
None
Maintainer
Reid F. Thompson <reid.thompson@gmail.com>
License
GPL (>= 2)
Version
1.32.0

View on Bioconductor

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

Files in this package

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