AbstractCNData | The AbstractCNData class |
AbstractPSCNData | The AbstractPSCNData class |
allocate.AromaTabularBinaryFile | Creates an AromaTabularBinaryFile |
AromaCellCpgFile | A binary file holding local CpG density for each cell... |
AromaCellPositionFile | A binary file holding chromosome/position for each cell |
AromaCellTabularBinaryFile | The AromaCellTabularBinaryFile class |
aroma.core-package | Package aroma.core |
AromaGenomeTextFile | The AromaGenomeTextFile class |
AromaMicroarrayDataFile | The abstract AromaMicroarrayDataFile class |
AromaMicroarrayDataSet | The AromaMicroarrayDataSet class |
AromaMicroarrayDataSetTuple | The AromaMicroarrayDataSetTuple class |
AromaMicroarrayTabularBinaryFile | The AromaMicroarrayTabularBinaryFile class |
AromaPlatform | The AromaPlatform class |
AromaPlatformInterface | The AromaPlatformInterface class |
AromaRepository | The AromaRepository class |
AromaTabularBinaryFile | The AromaTabularBinaryFile class |
AromaTabularBinarySet | The AromaTabularBinarySet class |
AromaTransform | The AromaTransform class |
AromaUnitCallFile | The AromaUnitCallFile class |
AromaUnitCallSet | The AromaUnitCallSet class |
AromaUnitFracBCnBinaryFile | The AromaUnitFracBCnBinaryFile class |
AromaUnitFracBCnBinarySet | The AromaUnitFracBCnBinarySet class |
AromaUnitGenotypeCallFile | The AromaUnitGenotypeCallFile class |
AromaUnitGenotypeCallSet | The AromaUnitGenotypeCallSet class |
AromaUnitPscnBinaryFile | The AromaUnitPscnBinaryFile class |
AromaUnitPscnBinarySet | The AromaUnitPscnBinarySet class |
AromaUnitSignalBinaryFile | The AromaUnitSignalBinaryFile class |
AromaUnitSignalBinarySet | The AromaUnitSignalBinarySet class |
AromaUnitTabularBinaryFile | The AromaUnitTabularBinaryFile class |
AromaUnitTotalCnBinaryFile | The AromaUnitTotalCnBinaryFile class |
AromaUnitTotalCnBinarySet | The AromaUnitTotalCnBinarySet class |
AromaUnitTypesFile | The AromaUnitTypesFile class |
as.GrayscaleImage.matrix | Creates a Grayscale (Color) Image from a matrix file |
BinnedScatter | The BinnedScatter class |
CacheKeyInterface | The CacheKeyInterface class interface |
CbsModel | The CbsModel class |
ChromosomalModel | The ChromosomalModel class |
ChromosomeExplorer | The ChromosomeExplorer class |
colBinnedSmoothing.matrix | Binned smoothing of a matrix column by column |
colKernelSmoothing.matrix | Kernel smoothing of a matrix column by column |
CopyNumberChromosomalModel | The CopyNumberChromosomalModel class |
CopyNumberSegmentationModel | The CopyNumberSegmentationModel class |
display.Explorer | Displays the explorer in the default browser |
doCBS | Performs Circular Binary Segmentation (CBS) on a data set |
downloadChipTypeFile.AromaRepository | Download a particular chip type annotation file |
downloadFile.AromaRepository | Download a particular file from the repository |
estimateSds.CopyNumberChromosomalModel | Estimates the standard deviation of the raw copy numbers... |
estimateStandardDeviation.RawGenomicSignals | Estimates the standard deviation of the raw Ys |
Explorer | The Explorer class |
exportAromaUnitPscnBinarySet | Export total and allele B signal data sets as a unified... |
extractRawCopyNumbers.CopyNumberChromosomalModel | Extracts relative copy numbers |
FileCacheKeyInterface | The FileCacheKeyInterface class interface |
findAnnotationData | Locates an annotation data file |
findAnnotationDataByChipType | Locates an annotation data file by its chip type |
findFilesTodo.AromaTransform | Finds files in the data set still not processed |
fit.CopyNumberChromosomalModel | Fits the model |
fit.CopyNumberSegmentationModel | Fits the model |
fitGenotypeConeBySfit.matrix | Fits an affine transformation to allele A and allele B data |
fitGenotypeCone.matrix | Fits an affine transformation to allele A and allele B data |
fitMultiDimensionalCone.matrix | Fits an affine transformation to multi-dimensional data |
getAlias.Explorer | Gets the alias of the output set |
getAromaPlatform.AromaPlatformInterface | Gets the platform |
getCacheKey.CacheKeyInterface | Gets a list of cache key items |
getCacheKey.FileCacheKeyInterface | Gets a list of cache key items |
getChipType.AromaPlatformInterface | Gets the chip type |
getChipType.ChromosomalModel | Gets a label for all chip types merged |
getChromosomes.ChromosomalModel | Gets the chromosomes to be processed |
getChromosomes.ChromosomeExplorer | Gets the chromosomes available |
getFullName.AromaTransform | Gets the full name of the output data set |
getInputDataSet.AromaTransform | Gets the input data set |
getModel.ChromosomeExplorer | Gets the model |
getName.AromaTransform | Gets the name of the output data set |
getName.Explorer | Gets the name of the explorer |
getNames.ChromosomalModel | Gets the names of the arrays |
getNames.Explorer | Gets the names of the input samples |
getOutputDataSet.AromaTransform | Gets the transformed data set |
getParametersAsString.ParametersInterface | Gets the parameters as character |
getParameters.ParametersInterface | Gets a list of parameters |
getPath.AromaTransform | Gets the path of the output directory |
getPath.Explorer | Gets the path of the output directory |
getPlatform.AromaPlatformInterface | Gets the platform |
getRootPath.AromaTransform | Gets the root path of the output directory |
getRootPath.Explorer | Gets the root path of the output directory |
getTags.AromaTransform | Gets the tags of the output data set |
getTags.Explorer | Gets the tags of the explorer |
getUnitAnnotationDataFile.AromaPlatformInterface | Gets a unit annotation data file of a particular class |
GladModel | The GladModel class |
HaarSegModel | The HaarSegModel class |
indexOf.UnitNamesFile | Gets the indices of units by their names |
isCompatibleWith.AromaPlatformInterface | Checks if a particular unit annotation data file is... |
isDone.AromaTransform | Checks if the data set is processed or not |
listFiles.AromaRepository | Retrieves the files available on the repository under a... |
matrixBlockPolish.matrix | Applies a polishing function to blocks of rows and columns... |
mergeBoxplotStats.list | Merges a list of boxplot.stats() elements |
nbrOfArrays.ChromosomalModel | Gets the number of arrays |
nbrOfArrays.Explorer | Gets the total number of arrays |
nbrOfChipTypes.AromaMicroarrayDataSetTuple | Gets the number of chip types |
nbrOfChipTypes.ChromosomalModel | Gets the number of chip types |
Non-documented_objects | Non-documented objects |
NonPairedPSCNData | The NonPairedPSCNData class |
PairedPSCNData | The PairedPSCNData class |
ParametersInterface | The ParametersInterface class interface |
plotTracks.PairedPSCNData | Plots parental specific copy numbers along the genome |
process.AromaTransform | Processes the data set |
process.ChromosomeExplorer | Generates image files, scripts and dynamic pages for the... |
process.Explorer | Generates image files, scripts and dynamic pages for the... |
processTime | Gets the running time of the R process and its children... |
RawAlleleBFractions | The RawAlleleBFractions class |
RawCopyNumberModel | The RawCopyNumberModel class |
RawCopyNumbers | The RawCopyNumbers class |
RawGenomicSignals | The RawGenomicSignals class |
RawMirroredAlleleBFractions | The RawMirroredAlleleBFractions class |
RawSequenceReads | The RawSequenceReads class |
readFooter.AromaTabularBinaryFile | Reads the file footer in XML format into a named nested list |
segmentByCBS.RawGenomicSignals | Segment copy numbers using the CBS method |
segmentByGLAD.RawGenomicSignals | Segment copy numbers using the GLAD method |
segmentByHaarSeg.RawGenomicSignals | Segment copy numbers using the HaarSeg method |
segmentByMPCBS.RawGenomicSignals | Segment copy numbers using the multi-platform CBS (mpCBS)... |
SegmentedAlleleBFractions | The SegmentedAlleleBFractions class |
SegmentedCopyNumbers | The SegmentedCopyNumbers class |
SegmentedGenomicSignalsInterface | The SegmentedGenomicSignalsInterface class interface |
setAlias.Explorer | Sets the alias of the output set |
setArrays.ChromosomeExplorer | Sets the arrays |
setArrays.Explorer | Sets the arrays |
UnitAnnotationDataFile | The UnitAnnotationDataFile interface class |
UnitNamesFile | The UnitNamesFile interface class |
UnitTypesFile | The UnitTypesFile interface class |
updateSetupExplorerFile.ChromosomeExplorer | Updates the Javascript file |
writeDataFrame.AromaUnitSignalBinaryFile | Writes the data file as a tab-delimited text file |
writeDataFrame.AromaUnitSignalBinarySet | Writes the data set as a tab-delimited text file |
writeDataFrame.AromaUnitTabularBinaryFile | Writes the data file as a tab-delimited text file |
writeFooter.AromaTabularBinaryFile | Writes a named nested list to the file footer in XML format |
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