A B C D E F G H I L M N O P R S T V W
oneChannelGUI-package | Set of functions extending the capability of affylmGUI 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 |
crosshybhuex10stv2na23hg18 | 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 |
crosshybmoex10stv1na23mm8 | 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 |
crosshybraex10stv1na23rn4 | 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 |
huex10stv2na23hg18 | 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 |
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 |
moex10stv1na23mm8 | 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 |
raex10stv1na23rn4 | 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 |
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 |
VennDiagram | Venn diagrams using two or three lists |
whichKindOfArray | Starting oneChannelGUI package |