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 |
.myrk | 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 |
cosieHscore | Parameters precalculated for the Affymetrix core human annotation subgroup from FMI Bioinformatics group and needed to correct SI |
cosieHsfull | Parameters precalculated for the Affymetrix full human annotation subgroup from FMI Bioinformatics group and needed to correct SI |
cosieMmcore | Parameters precalculated for the Affymetrix core mouse annotation subgroup from FMI Bioinformatics group and needed to correct SI |
cosieMmfull | Parameters precalculated for the Affymetrix full mouse annotation subgroup from FMI Bioinformatics group and needed to correct SI |
cosieWrapper | 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 |
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 hybridization 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 |
exonContrasts | Defining t-test regularized p-values |
exonsSpecific2as | Defining the exons associated to the various alternative isoforms |
exonTopTableExtract | Extracts data on the basis of a defined t-test regularized p-value |
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 |
huex.variantexons | table linking exon-level probe set ids to variant exons |
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 |
limmaExons | graphical interface to limma for alternative splicing detection |
listFilter | Subsetting an expression set using a list of Affymetrix ids |
makeBED15 | This function creates files in BED15 format to be loaded on the UCSC browser |
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 |
moex.variantexons | table linking exon-level probe set ids to variant exons |
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 |
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 |
plotVariantSI | This function plots on UCSC genome browser data derived by variantSI filter |
raex.annotation | Annotation data for CORE subset of rat exon array 1.0 ST |
raex.variantexons | table linking exon-level probe set ids to variant exons |
ragene.annotation | Annotation data for rat gene array 1.0 ST |
rankingConversion | This function transforms intensity data in normalized ranks |
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 |
runningJetta | graphical interface to MADS/jetta R library. |
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 |
variantExons | This function is used to generate a table containing exon-level probe set data linked to variant exons |
variantSI | This function allows filtering on the basis of variant exons |
VennDiagram | Venn diagrams using two or three lists |
whichKindOfArray | Starting oneChannelGUI package |