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A B C D E F G H I L M N O P R S T U V W
| oneChannelGUI-package | Set of functions extending the capability of affylmGUI package |
| .annotation | Starting oneChannelGUI package |
| AboutaffylmGUI | Starting oneChannelGUI package |
| AboutextendedaffylmGUI | Starting oneChannelGUI package |
| addAnnLib | Starting oneChannelGUI package |
| affyPLMHelp | Starting oneChannelGUI package |
| affyPlotMA | Starting oneChannelGUI package |
| aptFolder | Starting oneChannelGUI package |
| AptMidas | Graphical interface to APT midas |
| biomartFilter | Filtering only gene-level probe sets with multiple ensembl transcripts |
| buildingLocalAnnotation | Updates local gene-level annotation data for gene and exon arrays using the netaffx database |
| changeMenu | Starting oneChannelGUI package |
| changes | Starting oneChannelGUI package |
| chooseEDir | Starting oneChannelGUI package |
| colExtract | Extract a column from a tab delimited file with header |
| combineGeoMSF | This function allows to combine GEO Matrix Series Files belonging to the same experiment. |
| ComputeContrasts | Starting oneChannelGUI package |
| ComputeLinearModelFit | Starting oneChannelGUI package |
| consistentFilters | This function allows filtering using the combination of multiple paramenters, e.g. MiDAS p-values and Rank Product p-values |
| createGeoTarget | Creating a affylmGUI Target starting from a GEO Matrix series file |
| crosshybFilter | Removing from exon array gene/exon level probe sets characterized by cross hybridization with other transcripts |
| crosshybhuex.annotation | Cross hybriduzation data for exon CORE subset of human exon array 1.0 ST |
| crosshybmoex.annotation | Cross hybriduzation data for exon CORE subset of mouse exon array 1.0 ST |
| crosshybraex.annotation | Cross hybriduzation data for exon CORE subset of rat exon array 1.0 ST |
| dabgFilter | Starting oneChannelGUI package |
| delete.ML | Starting oneChannelGUI package |
| deleteLocalData | Starting oneChannelGUI package |
| dfMAplot | MA and Volcano plots from data present in a limma derived topTable |
| EG2probeset | This function allows to link GeneBank and Entrez Gene ids to gene-level probe set ids |
| erankProdAltSpl | Implementation of the Rank Product method for the detection of alternative splicing events |
| erankProdAltSplFilter | Filtering Rank Product results for the detection of alternative splicing events |
| exonsSpecific2as | Defining the exons associated to the various alternative isoforms |
| ExportfeatureNames | Starting oneChannelGUI package |
| ExportNormalizedExpressionValues | Starting oneChannelGUI package |
| ExportNormalizedExpressionValues1 | Starting oneChannelGUI package |
| extractAffyids | Extracting probe ids associated to a specific Gene Ontology term |
| filteringTable | Filtering a tab delimited file |
| geneExonLibs | Download the Library files for gene and exon analysis |
| genefilterHelp | Starting oneChannelGUI package |
| geoVSbioc | linking GEO platforms to available BioC annotations libraries |
| GetNormalizationMethod | Starting oneChannelGUI package |
| GOenrichment | Searching for Gene Ontology enriched terms within a set of differentially expressed genes |
| GOstatsHelp | Starting oneChannelGUI package |
| huex.annotation | Annotation data for CORE subset of human exon array 1.0 ST |
| hugene.annotation | Annotation data for human gene array 1.0 ST |
| initialize.extAffylmGUI | Starting oneChannelGUI package |
| inspecting.one.splice.index | Plotting on the profiles of splice indexes for a transcript cluster ID |
| inspecting.splice.index | Plotting on a pdf file the profiles of splice indexes |
| intensityFilter | intensity filtering with a mouse click |
| intronicBg | Starting oneChannelGUI package |
| IPAlistFilter | Filtering an expression set using a set of Entrez genes extracted from Ingenuity Pathways analysis (IPA) |
| iqrFilter | Interquantile filtering with a mouse click |
| largedatasetNorm | Starting oneChannelGUI package |
| libraryFilesDir | Starting oneChannelGUI package |
| listFilter | Subsetting an expression set using a list of Affymetrix ids |
| mapping2ensembl | Associating e-level probe sets to entrez gene exonic structure |
| mapping2exon | 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 |
| mapping2RefSeq | This function maps on NCBI Reference sequences spliced exons detected by the function oneChannelGUI: Inspecting splice indexes |
| masigpro | The function executes maSigPro analysis |
| masigpro.edesign | The function creates an edesign object needed to run maSigPro |
| masigpro.view | The function allows the visualization of maSigPro results |
| maSigProHelp | Starting oneChannelGUI package |
| metaArrayIC | Graphical interface to metaArray Integrative Correlation function |
| metaArrayMerge | Tool to create a merge object for metaArray package |
| midasFilter | Starting oneChannelGUI package |
| ML.edesign | The function creates an data frame containing the parameters useful for class prediction |
| moex.annotation | Annotation data for CORE subset of mouse exon array 1.0 ST |
| mogene.annotation | Annotation data for mouse gene array 1.0 ST |
| myExpresso | Running the affy expresso function with the widget |
| NewLimmaFile | Starting oneChannelGUI package |
| NormalizeNow | Starting oneChannelGUI package |
| normBoxplot | Box plot of the arrays data available in NormalizeAffyData slot |
| ocPlotHist | Gene/Exon level density plots |
| ocPlotPCA | Gene/Exon level density plots |
| oneChannelGUI | Set of functions extending the capability of affylmGUI package |
| oneChannelGUI.start | Starting oneChannelGUI package |
| oneChannelGUIHelp | Starting oneChannelGUI package |
| OpenAFile | Starting oneChannelGUI package |
| OpenAGeoFile | Starting oneChannelGUI package |
| OpenALimmaFile | Starting oneChannelGUI package |
| OpenBeadStudioFiles | Read BeadStudio expression data file |
| OpenCDFandTargetsfiles | Starting oneChannelGUI package |
| OpenExonandTargetsfiles | Starting oneChannelGUI package |
| OpenExonFile | Starting oneChannelGUI package |
| OpenExonProbeFile | Starting oneChannelGUI package |
| OpenGeoFile | Starting oneChannelGUI package |
| OpenGeoFiles | Starting oneChannelGUI package |
| OpenLargeFile | Starting oneChannelGUI package |
| OpenLargefiles | This function loads large data set made from tab delimited files |
| OpenLimmaFile | Starting oneChannelGUI package |
| pamrHelp | Starting oneChannelGUI package |
| pdmclassHelp | Starting oneChannelGUI package |
| plierToZero | Setting to 0 low log2 intensity values generated with plier |
| plotGO | Plotting parents of a GO term with few mouse click |
| PlotOptionsv1 | A modified version of the function used in affyPLM library |
| raex.annotation | Annotation data for CORE subset of rat exon array 1.0 ST |
| ragene.annotation | Annotation data for rat gene array 1.0 ST |
| rankProd | graphical interface to rank product method implemented in RankProd Bioconductor library. |
| RankProdHelp | Starting oneChannelGUI package |
| rawBoxplotPN | Plotting raw log2 intensities from controls |
| rawpCheck | Raw p-value distribution from limma analysis by a mouse click |
| recoverUnfiltered | Starting oneChannelGUI package |
| refseqDownload | Retrieving Reference Sequences from NCBI ftp |
| retrievePSRseq | This function, given a file containing exon-level probesets retrieves Probe selection Regions, PRS, from RRE db |
| reviqrFilter | Reverse interquantile filtering with a mouse click |
| sample.size.evaluation | The function executes and plots results from ssize and delta fulction from the ssize packahe |
| sample.size.evaluation1 | The function executes functions from the sizepower packahe |
| SaveAsLimmaFile | Starting oneChannelGUI package |
| SetED | Starting oneChannelGUI package |
| showDataset | Grabbing info about the available expression set |
| showTopTable | Modification of the function immplemented in affylmGUI to generate a topTable |
| siggenes | The function executes SAM analysis implemented in siggenes bioconductor library |
| siggenesHelp | Starting oneChannelGUI package |
| simFilter | This function allows filtering on the basis of the average splice index mean or min difference between two groups |
| sizepowerHelp | Starting oneChannelGUI package |
| spliceIndex | This function coverts the exon intenisty data in a slice index |
| ssizeHelp | Starting oneChannelGUI package |
| targetWidget | Widget to create a target file to load .CEL files |
| templA | Generating a template A to be uploaded in Ingenuity Pathways analysis (IPA) |
| trainTest | Creating a training set and a test set by a mouse click |
| updateLibs | This function allows to update the present installation of Bioconductor |
| VennDiagram | Venn diagrams using two or three lists |
| whichKindOfArray | Starting oneChannelGUI package |