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HELP (version 1.30.0)

Tools for HELP data analysis

Description

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

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Version

Version

1.30.0

License

GPL (>= 2)

Maintainer

Reid F Thompson

Last Published

February 15th, 2017

Functions in HELP (1.30.0)

calcPrototype

Calculate prototype
calcTm-methods

Calculate Tm (methods)
fuzzyMatches-methods

Fuzzy matching (methods)
exprs2

Retrieve microarray data (for signal channel 2) from ExpressionSets
plotPairs

Plot tree-pairs
quantileNormalize-methods

Quantile normalization (methods)
calcGC

Calculate GC percent
fuzzyMatches

Fuzzy matching
calcPrototype-methods

Calculate prototype (methods)
getFeatures-methods

Get features (methods)
base.stacking.thermodynamics

Base-stacking thermodynamic parameters
calcGC-methods

Calculate GC percent (methods)
getSamples

Get samples
plotBins-methods

Plot bins (methods)
quantileNormalize

Quantile normalization
readDesign-methods

Read NimbleGen design files (methods)
createWiggle

Create wiggle track
exprs2-methods

Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)
plotPairs-methods

Plot tree-pairs (methods)
readDesign

Read NimbleGen design files
plotFeature

Plot feature versus two-color intensity
readPairs-methods

Read Nimblegen .pair files (methods)
calcTm

Calculate Tm
combineData-methods

Combine data (methods)
getFeatures

Get features (methods)
getSamples-methods

Get samples (methods)
plotChip-methods

Plot chip image (methods)
readPairs

Read Nimblegen .pair files
plotBins

Plot bins
readSampleKey

Read sample key
combineData

Combine data
plotChip

Plot chip image
createWiggle-methods

Create wiggle track (methods)
plotFeature-methods

Plot feature versus two-color intensity (methods)