Name Mode Size
..
000.R 100644 0 kb
901.CalibrationAndNormalization.R 100644 10 kb
999.NonDocumentedObjects.R 100644 1 kb
999.package.R 100644 4 kb
averageQuantile.R 100644 5 kb
backtransformAffine.R 100644 6 kb
backtransformPrincipalCurve.R 100644 7 kb
backtransformXYCurve.matrix.R 100644 1 kb
calibrateMultiscan.R 100644 10 kb
callNaiveGenotypes.R 100644 7 kb
distanceBetweenLines.R 100644 4 kb
findPeaksAndValleys.R 100644 4 kb
fitIWPCA.R 100644 15 kb
fitNaiveGenotypes.R 100644 8 kb
fitPrincipalCurve.R 100644 5 kb
fitXYCurve.R 100644 7 kb
iwpca.R 100644 9 kb
likelihood.smooth.spline.R 100644 6 kb
linearAlgebra.R 100644 1 kb
lines.XYCurveFit.R 100644 0 kb
medianPolish.R 100644 5 kb
normalizeAffine.R 100644 9 kb
normalizeAverage.R 100644 2 kb
normalizeCurveFit.R 100644 11 kb
normalizeDifferencesToAverage.R 100644 2 kb
normalizeFragmentLength.R 100644 14 kb
normalizeQuantileRank.R 100644 6 kb
normalizeQuantileRank.matrix.R 100644 10 kb
normalizeQuantileSpline.R 100644 8 kb
normalizeTumorBoost.R 100644 11 kb
pairedAlleleSpecificCopyNumbers.R 100644 5 kb
plotDensity.R 100644 7 kb
plotMvsA.R 100644 2 kb
plotMvsAPairs.R 100644 3 kb
plotMvsMPairs.R 100644 2 kb
plotXYCurve.R 100644 5 kb
predict.lowess.R 100644 0 kb
print.SmoothSplineLikelihood.R 100644 2 kb
robustSmoothSpline.R 100644 11 kb
rowAverages.matrix.R 100644 2 kb
sampleCorrelations.matrix.R 100644 4 kb
sampleTuples.R 100644 2 kb
wpca.R 100644 10 kb
zzz.R 100644 0 kb
README.md
<div id="badges"><!-- pkgdown markup --> <a href="https://bioconductor.org/packages/aroma.light/"><img border="0" src="https://bioconductor.org/shields/years-in-bioc/aroma.light.svg" alt="Bioconductor since badge"/></a> <a href="https://bioconductor.org/checkResults/release/bioc-LATEST/aroma.light/"><img border="0" src="https://bioconductor.org/shields/build/release/bioc/aroma.light.svg" alt="Bioconductor build status"/></a> <a href="https://bioconductor.org/checkResults/devel/bioc-LATEST/aroma.light/"><img border="0" src="https://bioconductor.org/shields/build/devel/bioc/aroma.light.svg" alt="Bioconductor build status"/></a> <a href="https://github.com/HenrikBengtsson/aroma.light/actions?query=workflow%3AR-CMD-check"><img border="0" src="https://github.com/HenrikBengtsson/aroma.light/actions/workflows/R-CMD-check.yaml/badge.svg?branch=develop" alt="R CMD check status"/></a> <a href="https://app.codecov.io/gh/HenrikBengtsson/aroma.light"><img border="0" src="https://codecov.io/gh/HenrikBengtsson/aroma.light/branch/develop/graph/badge.svg" alt="Coverage Status"/></a> </div> # aroma.light: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types ## Installation R package aroma.light is available on [Bioconductor](https://www.bioconductor.org/packages/devel/bioc/html/aroma.light.html) and can be installed in R as: ```r install.packages("BiocManager") BiocManager::install("aroma.light") ``` ### Pre-release version To install the pre-release version that is available in Git branch `develop` on GitHub, use: ```r remotes::install_github("HenrikBengtsson/aroma.light", ref="develop") ``` This will install the package from source. <!-- pkgdown-drop-below --> ## Contributing To contribute to this package, please see [CONTRIBUTING.md](CONTRIBUTING.md).