# Tools for HELP data analysis

## Documentation for package ‘HELP’ version 1.60.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

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