Entry: AptMidas
Aliases: AptMidas
Keywords: manip
Description: Graphical interface to APT midas
URL: ../../../library/oneChannelGUI/html/AptMidas.html

Entry: EG2probeset
Aliases: EG2probeset
Keywords: manip
Description: This function allows to link GeneBank and Entrez Gene ids to gene-level probe set ids
URL: ../../../library/oneChannelGUI/html/EG2probeset.html

Entry: GOenrichment
Aliases: GOenrichment
Keywords: methods
Description: Searching for Gene Ontology enriched terms within a set of differentially expressed genes
URL: ../../../library/oneChannelGUI/html/GOenrichment.html

Entry: IPAlistFilter
Aliases: IPAlistFilter
Keywords: methods
Description: Filtering an expression set using a set of Entrez genes extracted from Ingenuity Pathways analysis (IPA)
URL: ../../../library/oneChannelGUI/html/IPAlistFilter.html

Entry: ML.edesign
Aliases: ML.edesign
Keywords: utilities
Description: The function creates an data frame containing the parameters useful for class prediction
URL: ../../../library/oneChannelGUI/html/ML.edesign.html

Entry: OpenBeadStudioFiles
Aliases: OpenBeadStudioFiles
Keywords: methods
Description: Read BeadStudio expression data file
URL: ../../../library/oneChannelGUI/html/OpenBeadStudioFiles.html

Entry: OpenLargefiles
Aliases: OpenLargefiles
Keywords: utilities
Description: This function loads large data set made from tab delimited files
URL: ../../../library/oneChannelGUI/html/OpenLargefiles.html

Entry: PlotOptionsv1
Aliases: PlotOptionsv1
Keywords: methods
Description: A modified version of the function used in affyPLM library
URL: ../../../library/oneChannelGUI/html/PlotOptionsv1.html

Entry: VennDiagram
Aliases: VennDiagram
Keywords: hplot
Description: Venn diagrams using two or three lists
URL: ../../../library/oneChannelGUI/html/VennDiagram.html

Entry: biomartFilter
Aliases: biomartFilter
Keywords: manip
Description: Filtering only gene-level probe sets with multiple ensembl transcripts
URL: ../../../library/oneChannelGUI/html/biomartFilter.html

Entry: buildingLocalAnnotation
Aliases: buildingLocalAnnotation
Keywords: methods
Description: Updates local gene-level annotation data for gene and exon arrays using the netaffx database
URL: ../../../library/oneChannelGUI/html/buildingLocalAnnotation.html

Entry: colExtract
Aliases: colExtract
Keywords: manip
Description: Extract a column from a tab delimited file with header
URL: ../../../library/oneChannelGUI/html/colExtract.html

Entry: combineGeoMSF
Aliases: combineGeoMSF
Keywords: methods
Description: This function allows to combine GEO Matrix Series Files belonging to the same experiment.
URL: ../../../library/oneChannelGUI/html/combineGeoMSF.html

Entry: consistentFilters
Aliases: consistentFilters
Keywords: manip
Description: This function allows filtering using the combination of multiple paramenters, e.g. MiDAS p-values and Rank Product p-values
URL: ../../../library/oneChannelGUI/html/consistentFilters.html

Entry: cosieHscore
Aliases: cosieHscore
Keywords: datasets
Description: Parameters precalculated for the Affymetrix core human annotation subgroup from FMI Bioinformatics group and needed to correct SI
URL: ../../../library/oneChannelGUI/html/cosieHscore.html

Entry: cosieHsfull
Aliases: cosieHsfull
Keywords: datasets
Description: Parameters precalculated for the Affymetrix full human annotation subgroup from FMI Bioinformatics group and needed to correct SI
URL: ../../../library/oneChannelGUI/html/cosieHsfull.html

Entry: cosieMmcore
Aliases: cosieMmcore
Keywords: datasets
Description: Parameters precalculated for the Affymetrix core mouse annotation subgroup from FMI Bioinformatics group and needed to correct SI
URL: ../../../library/oneChannelGUI/html/cosieMmcore.html

Entry: cosieMmfull
Aliases: cosieMmfull
Keywords: datasets
Description: Parameters precalculated for the Affymetrix full mouse annotation subgroup from FMI Bioinformatics group and needed to correct SI
URL: ../../../library/oneChannelGUI/html/cosieMmfull.html

Entry: cosieWrapper
Aliases: cosieWrapper
Keywords: manip
Description: A wrapper to cosie, Corrected Splicing Indices for Exon arrays, that for any given set of new exon array experiments corrects for the observed bias and improves the detection of alternative splicing
URL: ../../../library/oneChannelGUI/html/cosieWrapper.html

Entry: createGeoTarget
Aliases: createGeoTarget
Keywords: methods
Description: Creating a affylmGUI Target starting from a GEO Matrix series file
URL: ../../../library/oneChannelGUI/html/createGeoTarget.html

Entry: crosshybFilter
Aliases: crosshybFilter
Keywords: methods
Description: Removing from exon array gene/exon level probe sets characterized by cross hybridization with other transcripts
URL: ../../../library/oneChannelGUI/html/crosshybFilter.html

Entry: crosshybhuex.annotation
Aliases: crosshybhuex.annotation
Keywords: datasets
Description: Cross hybriduzation data for exon CORE subset of human exon array 1.0 ST
URL: ../../../library/oneChannelGUI/html/crosshybhuex.annotation.html

Entry: crosshybmoex.annotation
Aliases: crosshybmoex.annotation
Keywords: datasets
Description: Cross hybriduzation data for exon CORE subset of mouse exon array 1.0 ST
URL: ../../../library/oneChannelGUI/html/crosshybmoex.annotation.html

Entry: crosshybraex.annotation
Aliases: crosshybraex.annotation
Keywords: datasets
Description: Cross hybridization data for exon CORE subset of rat exon array 1.0 ST
URL: ../../../library/oneChannelGUI/html/crosshybraex.annotation.html

Entry: dfMAplot
Aliases: dfMAplot
Keywords: hplot methods
Description: MA and Volcano plots from data present in a limma derived topTable
URL: ../../../library/oneChannelGUI/html/dfMAplot.html

Entry: erankProdAltSpl
Aliases: erankProdAltSpl
Keywords: manip
Description: Implementation of the Rank Product method for the detection of alternative splicing events
URL: ../../../library/oneChannelGUI/html/erankProdAltSpl.html

Entry: erankProdAltSplFilter
Aliases: erankProdAltSplFilter
Keywords: manip
Description: Filtering Rank Product results for the detection of alternative splicing events
URL: ../../../library/oneChannelGUI/html/erankProdAltSplFilterl.html

Entry: exonContrasts
Aliases: exonContrasts
Keywords: utilities
Description: Defining t-test regularized p-values
URL: ../../../library/oneChannelGUI/html/exonContrasts.html

Entry: exonTopTableExtract
Aliases: exonTopTableExtract
Keywords: utilities
Description: Extracts data on the basis of a defined t-test regularized p-value
URL: ../../../library/oneChannelGUI/html/exonTopTableExtract.html

Entry: exonsSpecific2as
Aliases: exonsSpecific2as
Keywords: manip
Description: Defining the exons associated to the various alternative isoforms
URL: ../../../library/oneChannelGUI/html/exonsSpecific2as.html

Entry: extractAffyids
Aliases: extractAffyids
Keywords: methods
Description: Extracting probe ids associated to a specific Gene Ontology term
URL: ../../../library/oneChannelGUI/html/extractAffyids.html

Entry: filteringTable
Aliases: filteringTable
Keywords: manip
Description: Filtering a tab delimited file
URL: ../../../library/oneChannelGUI/html/filteringTable.html

Entry: geneExonLibs
Aliases: geneExonLibs
Keywords: methods
Description: Download the Library files for gene and exon analysis
URL: ../../../library/oneChannelGUI/html/geneExonLibs.html

Entry: geoVSbioc
Aliases: geoVSbioc
Keywords: datasets
Description: linking GEO platforms to available BioC annotations libraries
URL: ../../../library/oneChannelGUI/html/geoVSbioc.html

Entry: huex.annotation
Aliases: huex.annotation
Keywords: datasets
Description: Annotation data for CORE subset of human exon array 1.0 ST
URL: ../../../library/oneChannelGUI/html/huex.annotation.html

Entry: huex.variantexons
Aliases: huex.variantexons
Keywords: datasets
Description: table linking exon-level probe set ids to variant exons
URL: ../../../library/oneChannelGUI/html/huex.variantexons.html

Entry: hugene.annotation
Aliases: hugene.annotation
Keywords: datasets
Description: Annotation data for human gene array 1.0 ST
URL: ../../../library/oneChannelGUI/html/hugene.annotation.html

Entry: inspecting.one.splice.index
Aliases: inspecting.one.splice.index
Keywords: methods
Description: Plotting on the profiles of splice indexes for a transcript cluster ID
URL: ../../../library/oneChannelGUI/html/inspecting.one.splice.index.html

Entry: inspecting.splice.index
Aliases: inspecting.splice.index
Keywords: methods
Description: Plotting on a pdf file the profiles of splice indexes
URL: ../../../library/oneChannelGUI/html/inspecting.splice.index.html

Entry: intensityFilter
Aliases: intensityFilter
Keywords: methods
Description: intensity filtering with a mouse click
URL: ../../../library/oneChannelGUI/html/intensityFilter.html

Entry: iqrFilter
Aliases: iqrFilter
Keywords: methods
Description: Interquantile filtering with a mouse click
URL: ../../../library/oneChannelGUI/html/iqrFilter.html

Entry: limmaExons
Aliases: limmaExons
Keywords: utilities
Description: graphical interface to limma for alternative splicing detection
URL: ../../../library/oneChannelGUI/html/limmaExons.html

Entry: listFilter
Aliases: listFilter
Keywords: methods
Description: Subsetting an expression set using a list of Affymetrix ids
URL: ../../../library/oneChannelGUI/html/listFilter.html

Entry: makeBED15
Aliases: makeBED15
Keywords: manip
Description: This function creates files in BED15 format to be loaded on the UCSC browser
URL: ../../../library/oneChannelGUI/html/makeBED15.html

Entry: mapping2RefSeq
Aliases: mapping2RefSeq
Keywords: manip
Description: This function maps on NCBI Reference sequences spliced exons detected by the function oneChannelGUI: Inspecting splice indexes
URL: ../../../library/oneChannelGUI/html/mapping2RefSeq.html

Entry: mapping2ensembl
Aliases: mapping2ensembl
Keywords: manip
Description: Associating e-level probe sets to entrez gene exonic structure
URL: ../../../library/oneChannelGUI/html/mapping2ensembl.html

Entry: mapping2exon
Aliases: mapping2exon
Keywords: manip
Description: This function maps on exon-level Probe Selection Region (PSR) starting for the file produced by function oneChannelGUI: Mapping exon level probe sets to Reference Sequences
URL: ../../../library/oneChannelGUI/html/mapping2exon.html

Entry: masigpro
Aliases: masigpro
Keywords: utilities
Description: The function executes maSigPro analysis
URL: ../../../library/oneChannelGUI/html/masigpro.html

Entry: masigpro.edesign
Aliases: masigpro.edesign
Keywords: utilities
Description: The function creates an edesign object needed to run maSigPro
URL: ../../../library/oneChannelGUI/html/masigpro.edesign.html

Entry: masigpro.view
Aliases: masigpro.view
Keywords: utilities
Description: The function allows the visualization of maSigPro results
URL: ../../../library/oneChannelGUI/html/masigpro.view.html

Entry: metaArrayIC
Aliases: metaArrayIC
Keywords: manip
Description: Graphical interface to metaArray Integrative Correlation function
URL: ../../../library/oneChannelGUI/html/metaArrayIC.html

Entry: metaArrayMerge
Aliases: metaArrayMerge
Keywords: manip
Description: Tool to create a merge object for metaArray package
URL: ../../../library/oneChannelGUI/html/metaArrayMerge.html

Entry: moex.annotation
Aliases: moex.annotation
Keywords: datasets
Description: Annotation data for CORE subset of mouse exon array 1.0 ST
URL: ../../../library/oneChannelGUI/html/moex.annotation.html

Entry: moex.variantexons
Aliases: moex.variantexons
Keywords: datasets
Description: table linking exon-level probe set ids to variant exons
URL: ../../../library/oneChannelGUI/html/moex.variantexons.html

Entry: mogene.annotation
Aliases: mogene.annotation
Keywords: datasets
Description: Annotation data for mouse gene array 1.0 ST
URL: ../../../library/oneChannelGUI/html/mogene.annotation.html

Entry: myExpresso
Aliases: myExpresso
Keywords: utilities
Description: Running the affy expresso function with the widget
URL: ../../../library/oneChannelGUI/html/myExpresso.html

Entry: normBoxplot
Aliases: normBoxplot
Keywords: hplot
Description: Box plot of the arrays data available in NormalizeAffyData slot
URL: ../../../library/oneChannelGUI/html/normBoxplot.html

Entry: ocPlotHist
Aliases: ocPlotHist
Keywords: utilities
Description: Gene/Exon level density plots
URL: ../../../library/oneChannelGUI/html/ocPlotHist.html

Entry: ocPlotPCA
Aliases: ocPlotPCA
Keywords: utilities
Description: Gene/Exon level density plots
URL: ../../../library/oneChannelGUI/html/ocPlotPCA.html

Entry: oneChannelGUI-package
Aliases: oneChannelGUI-package oneChannelGUI
Keywords: package
Description: Set of functions extending the capability of affylmGUI package
URL: ../../../library/oneChannelGUI/html/oneChannelGUI-package.html

Entry: oneChannelGUI
Aliases: AboutextendedaffylmGUI AboutaffylmGUI maSigProHelp siggenesHelp oneChannelGUIHelp initialize.extAffylmGUI OpenExonandTargetsfiles GOstatsHelp oneChannelGUIHelp NewLimmaFile OpenAFile OpenALimmaFile OpenLimmaFile OpenExonFile OpenExonProbeFile OpenLargeFile changeMenu oneChannelGUI.start libraryFilesDir whichKindOfArray intronicBg ExportNormalizedExpressionValues1 ExportNormalizedExpressionValues ExportfeatureNames SaveAsLimmaFile addAnnLib OpenCDFandTargetsfiles ComputeLinearModelFit GetNormalizationMethod NormalizeNow ComputeContrasts midasFilter dabgFilter largedatasetNorm RankProdHelp affyPLMHelp genefilterHelp pamrHelp pdmclassHelp sizepowerHelp ssizeHelp OpenAGeoFile OpenGeoFile OpenGeoFiles recoverUnfiltered delete.ML affyPlotMA changes aptFolder deleteLocalData SetED chooseEDir .annotation .myrk
Keywords: IO
Description: Starting oneChannelGUI package
URL: ../../../library/oneChannelGUI/html/oneChannelGUI.html

Entry: plierToZero
Aliases: plierToZero
Keywords: manip
Description: Setting to 0 low log2 intensity values generated with plier
URL: ../../../library/oneChannelGUI/html/plierToZero.html

Entry: plotGO
Aliases: plotGO
Keywords: hplot
Description: Plotting parents of a GO term with few mouse click
URL: ../../../library/oneChannelGUI/html/plotGO.html

Entry: plotVariantSI
Aliases: plotVariantSI
Keywords: manip
Description: This function plots on UCSC genome browser data derived by variantSI filter
URL: ../../../library/oneChannelGUI/html/plotVariantSI.html

Entry: raex.annotation
Aliases: raex.annotation
Keywords: datasets
Description: Annotation data for CORE subset of rat exon array 1.0 ST
URL: ../../../library/oneChannelGUI/html/raex.annotation.html

Entry: raex.variantexons
Aliases: raex.variantexons
Keywords: datasets
Description: table linking exon-level probe set ids to variant exons
URL: ../../../library/oneChannelGUI/html/raex.variantexons.html

Entry: ragene.annotation
Aliases: ragene.annotation
Keywords: datasets
Description: Annotation data for rat gene array 1.0 ST
URL: ../../../library/oneChannelGUI/html/ragene.annotation.html

Entry: rankProd
Aliases: rankProd
Keywords: utilities
Description: graphical interface to rank product method implemented in RankProd Bioconductor library.
URL: ../../../library/oneChannelGUI/html/rankProd.html

Entry: rankingConversion
Aliases: rankingConversion
Keywords: manip
Description: This function transforms intensity data in normalized ranks
URL: ../../../library/oneChannelGUI/html/rankingConversion.html

Entry: rawBoxplotPN
Aliases: rawBoxplotPN
Keywords: manip
Description: Plotting raw log2 intensities from controls
URL: ../../../library/oneChannelGUI/html/rawBoxplotPN.html

Entry: rawpCheck
Aliases: rawpCheck
Keywords: hplot
Description: Raw p-value distribution from limma analysis by a mouse click
URL: ../../../library/oneChannelGUI/html/rawpCheck.html

Entry: refseqDownload
Aliases: refseqDownload
Keywords: manip
Description: Retrieving Reference Sequences from NCBI ftp
URL: ../../../library/oneChannelGUI/html/refseqDownload.html

Entry: retrievePSRseq
Aliases: retrievePSRseq
Keywords: manip
Description: This function, given a file containing exon-level probesets retrieves Probe selection Regions, PRS, from RRE db
URL: ../../../library/oneChannelGUI/html/retrievePSRseq.html

Entry: reviqrFilter
Aliases: reviqrFilter
Keywords: methods
Description: Reverse interquantile filtering with a mouse click
URL: ../../../library/oneChannelGUI/html/reviqrFilter.html

Entry: runningJetta
Aliases: runningJetta
Keywords: utilities
Description: graphical interface to MADS/jetta R library.
URL: ../../../library/oneChannelGUI/html/runningJetta.html

Entry: sample.size.evaluation
Aliases: sample.size.evaluation
Keywords: utilities
Description: The function executes and plots results from ssize and delta fulction from the ssize packahe
URL: ../../../library/oneChannelGUI/html/sample.size.evaluation.html

Entry: sample.size.evaluation1
Aliases: sample.size.evaluation1
Keywords: utilities
Description: The function executes functions from the sizepower packahe
URL: ../../../library/oneChannelGUI/html/sample.size.evaluation1.html

Entry: showDataset
Aliases: showDataset
Keywords: methods
Description: Grabbing info about the available expression set
URL: ../../../library/oneChannelGUI/html/showDataset.html

Entry: showTopTable
Aliases: showTopTable
Keywords: methods
Description: Modification of the function immplemented in affylmGUI to generate a topTable
URL: ../../../library/oneChannelGUI/html/showTopTable.html

Entry: siggenes
Aliases: siggenes
Keywords: utilities
Description: The function executes SAM analysis implemented in siggenes bioconductor library
URL: ../../../library/oneChannelGUI/html/siggenes.html

Entry: simFilter
Aliases: simFilter
Keywords: manip
Description: This function allows filtering on the basis of the average splice index mean or min difference between two groups
URL: ../../../library/oneChannelGUI/html/simFilter.html

Entry: spliceIndex
Aliases: spliceIndex
Keywords: methods
Description: This function coverts the exon intenisty data in a slice index
URL: ../../../library/oneChannelGUI/html/spliceIndex.html

Entry: targetWidget
Aliases: targetWidget
Keywords: utilities
Description: Widget to create a target file to load .CEL files
URL: ../../../library/oneChannelGUI/html/targetWidget.html

Entry: templA
Aliases: templA
Keywords: methods
Description: Generating a template A to be uploaded in Ingenuity Pathways analysis (IPA)
URL: ../../../library/oneChannelGUI/html/templA.html

Entry: trainTest
Aliases: trainTest
Keywords: utilities
Description: Creating a training set and a test set by a mouse click
URL: ../../../library/oneChannelGUI/html/trainTest.html

Entry: updateLibs
Aliases: updateLibs
Keywords: methods
Description: This function allows to update the present installation of Bioconductor
URL: ../../../library/oneChannelGUI/html/updateLibs.html

Entry: variantExons
Aliases: variantExons
Keywords: methods
Description: This function is used to generate a table containing exon-level probe set data linked to variant exons
URL: ../../../library/oneChannelGUI/html/variantExons.html

Entry: variantSI
Aliases: variantSI
Keywords: manip
Description: This function allows filtering on the basis of variant exons
URL: ../../../library/oneChannelGUI/html/variantSI.html
