Files in beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

README.md

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

src/beadarray.h

src/findAllOutliers.c

src/BASH.c

src/determiningGridPositions.c

src/imageProcessing.c

src/HULK.c

data/platformSigs.rda

data/metaTemplate.rda

R/plotTIFF.R R/beadLevelData_combine.R R/beadLevelData_sectionNames.R R/swathData_processData.R R/HULK.R R/swathData_genSwaths.R R/readIllumina.R R/reports.R R/expressionSetIllumina_channelNames.R R/beadLevelData_plotBeadLocations.R R/readTIFF.R R/swathData_assignToImage.R R/methods-beadRegistrationData.R R/ExpressionSetIllumina_calculateDetection.R R/appendHistory.R R/getnextXMLtoken.R R/beadLevelData_sectionData.R R/expressionSetIllumina_channel.R R/methods-ExpressionSetIllumina.R R/beadLevelData_summarize.R R/boxplot.R R/beadLevelData_showArrayMask.R R/beadLevelData_setWeights.R R/beadLevelData_metrics.R R/beadLevelData_backgroundCorrect.R R/analyseDirectory.R R/beadLevelData_[[.R R/readSampleSheet.R R/methods-limmaResults.R R/outlierMethods.R R/beadLevelData_assignSegments.R R/beadLevelData_spatialPlot.R R/beadLevelData_uniqueProbeList.R R/beadLevelData_show.R R/standardIlluminaChannels.R R/experimental.R R/readBeadSummaryData.R R/swathData_checkSwathStatus.R R/swathData_singleBeadIntensity.R R/nearNonDecodedRegion.R R/insertBeadData.R R/sampleSheet.R R/BASH.R R/ExpressionSetIlluminaPlotting.R R/beadLevelData_combinedQCPlot.R R/zzz.R R/beadLevelData_QC.R R/gridPositionsFromLocs.R R/beadLevelData_dim.R R/ExpressionSetIlluminaNormalisation.R R/limmaDE.R R/illuminaChannel_initialize.R R/AllClasses.R R/swathData_writeFiles.R R/beadLevelData_expressionQCPipeline.R R/createTargetsFile.R R/beadLevelData_outlierPlot.R R/imageplot.R R/imageProcessing.R R/miscFunctions.R R/readLocsFile.R R/GEO.R R/plotChipLayout.R R/obtainLocs.R R/readIdatFiles.R R/checkRegistration.R R/beadLevelData_getBeadData.R R/beadLevelData_numBeads.R R/convertBeadLevelList.R R/readBeadLevelTextFile.R R/annotation.R R/simpleXMLparse.R

vignettes/beadlevel.rnw

vignettes/beadarray.bib

vignettes/beadarray.rnw

vignettes/beadsummary.rnw

vignettes/ImageProcessing.rnw

man/summarize.Rd man/controlProbeDetection.Rd man/readBeadSummaryData.Rd man/insertBeadData.Rd man/medianNormalise.Rd man/boxplot.Rd man/readLocsFile.Rd man/generateNeighbours.Rd man/readIllumina.Rd man/annotationInterface.Rd man/beadarray-package.Rd man/beadarrayUsersGuide.Rd man/makeControlProfile.Rd man/imageplot.Rd man/class-limmaResults.Rd man/processSwathData.Rd man/class-BeadLevelList.Rd man/BASHExtended.Rd man/sampleSheet.Rd man/metrics.Rd man/squeezedVarOutlierMethod.Rd man/calculateOutlierStats.Rd man/class-ExpressionSetIllumina.Rd man/readIdatFiles.Rd man/transformationFunctions.Rd man/BASHCompact.Rd man/addFeatureData.Rd man/GEOtemplate.Rd man/plotMAXY.Rd man/imageProcessing.Rd man/platformSigs.Rd man/createTargetsFile.Rd man/sectionNames.Rd man/class-illuminaChannel.Rd man/noOutlierMethod.Rd man/BASH.Rd man/combine.Rd man/normaliseIllumina.Rd man/illuminaOutlierMethod.Rd man/convertBeadLevelList.Rd man/insertSectionData.Rd man/show.Rd man/setWeights.Rd man/class-beadRegistrationData.Rd man/showArrayMask.Rd man/poscontPlot.Rd man/outlierplot.Rd man/weightsOutlierMethod.Rd man/quickSummary.Rd man/expressionQCPipeline.Rd man/deprecatedFunctions.Rd man/identifyControlBeads.Rd man/calculateDetection.Rd man/makeQCTable.Rd man/plotChipLayout.Rd man/HULK.Rd man/maplots.Rd man/getBeadData.Rd man/plotBeadIntensities.Rd man/numBeads.Rd man/GEO.Rd man/limmaDE.Rd man/plotTIFF.Rd man/class-beadLevelData.Rd man/checkRegistration.Rd man/readTIFF.Rd man/BASHDiffuse.Rd man/plotBeadLocations.Rd man/dim.Rd man/backgroundCorrectSingleSection.Rd

inst/NEWS

inst/CITATION

inst/doc/beadlevel.rnw

inst/doc/ImageProcessing.pdf inst/doc/beadsummary.pdf inst/doc/ImageProcessing.R inst/doc/beadlevel.R

inst/doc/beadarray.rnw

inst/doc/beadsummary.rnw

inst/doc/beadarray.pdf inst/doc/beadlevel.pdf

inst/doc/ImageProcessing.rnw

inst/doc/beadsummary.R inst/doc/beadarray.R

beadarray documentation built on Nov. 8, 2020, 4:51 p.m.