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A B C D E F G H I J L M N O P Q R S T U V W misc
| oneChannelGUI-package | Set of functions extending the capability of affylmGUI package |
| AboutaffylmGUI | Starting oneChannelGUI package |
| AboutextendedaffylmGUI | Starting oneChannelGUI package |
| adaptorTrimm | Trimming 3,5 end primers for miRNAs NGS |
| addAnnLib | Starting oneChannelGUI package |
| addga | Starting oneChannelGUI package |
| affyPLMHelp | Starting oneChannelGUI package |
| affyPlotMA | Starting oneChannelGUI package |
| annotateNGSeset | Associate annotation to NGS data loaded in oneChannelGUI |
| aptFolder | Starting oneChannelGUI package |
| AptMidas | Graphical interface to APT midas |
| bayseqInterface | graphical interface to baySeq library. |
| biomartFilter | Filtering only gene-level probe sets with multiple ensembl transcripts |
| bofa | Bovine microRNA data set |
| bowtieBuilt | Downloading Bowtie prebuilt reference sets |
| bowtieDownload | Downloading Bowtie and Picard tools |
| bowtieGenomes | Downloading and building chromosome level genomes references for bowtie |
| buildingLocalAnnotation | Updates local gene-level annotation data for gene and exon arrays using the netaffx database |
| cdsDiff | TuxedoSuite |
| changeMenu | Starting oneChannelGUI package |
| changes | Starting oneChannelGUI package |
| chimeraseq | Starting oneChannelGUI package |
| chooseEDir | Starting oneChannelGUI package |
| chooseInDir | TuxedoSuite |
| chooseOutDir | TuxedoSuite |
| chrLength | Chromosomes lenghts |
| closePdf | 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. |
| combining2eSet | This function allows to combine two matrices extracted from oneChannelGUI. |
| 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 |
| 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 |
| createDir | TuxedoSuite |
| 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 |
| ctrtrtHeatmap | Creating heat map for maSigPro data with only one treatment condition |
| cuffdiff | TuxedoSuite |
| cufflinks | TuxedoSuite |
| cuffmerge | TuxedoSuite |
| dabgFilter | Starting oneChannelGUI package |
| delete.ML | Starting oneChannelGUI package |
| deleteLocalData | Starting oneChannelGUI package |
| desCounts | Starting oneChannelGUI package |
| DESeqInterface | Starting oneChannelGUI package |
| desGenes | desGenes |
| dexCounts | dexCounts |
| dexExons | dexExons |
| dfMAplot | MA and Volcano plots from data present in a limma derived topTable |
| EDAbetweenLane | Starting oneChannelGUI package |
| EDAbiasPlot | Starting oneChannelGUI package |
| EDAboxplot | Starting oneChannelGUI package |
| EDANtFreq | Plotting Nts frequency for mapped reads extracted from BAM files |
| EDAplotQuality | Plotting Quality scores for mapped reads extracted from BAM files |
| EDAreadNumber | Plotting the number of mapped reads extracted from BAM files |
| EDAwithinLane | Starting oneChannelGUI package |
| edgerInterface | graphical interface to edgeR library. |
| edgeRNorm | This function scale-normalize NGS raw data as described by Robinson and Oshlack Genome Biology 2010, 11:R25 |
| 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 |
| eSet4meV | This function allows to reformat an eSet to be loaded in meV visualization software |
| exonContrasts | Defining t-test regularized p-values |
| exonScaffold | stand alone function to generate a scaffold containing only exon location from ENSEMBL |
| exonsSpecific2as | Defining the exons associated to the various alternative isoforms |
| exonTopTableExtract | Extracts data on the basis of a defined t-test regularized p-value |
| exportFASTA | Starting oneChannelGUI package |
| ExportfeatureNames | Starting oneChannelGUI package |
| ExportNormalizedExpressionValues | Starting oneChannelGUI package |
| ExportNormalizedExpressionValues1 | Starting oneChannelGUI package |
| extPckInfo | Starting oneChannelGUI package |
| extractAffyids | Extracting probe ids associated to a specific Gene Ontology term |
| extractmirTargets | Extract miRNA targets showing a opposite regulation with respect to miRNA |
| fastQC | Starting oneChannelGUI package |
| filteringmiRtargets | Subsetting an expression set using a list of gene which are putative targets for a miRNA |
| filteringTable | Filtering a tab delimited file |
| fusionfilter | Starting oneChannelGUI package |
| fusionNS | Starting oneChannelGUI package |
| fusionpeptides | Starting oneChannelGUI package |
| geneDiff | TuxedoSuite |
| geneExonLibs | Download the Library files for gene and exon analysis |
| genefilterHelp | Starting oneChannelGUI package |
| genomePlot | This function plots average intensity signals for two group experiment over the genes and transcripts structure mapped on ENSEMBL to identify a specific splicing event |
| genomeStudioReformat | The present function reformat an expression file exported by Genome Studio in a format that is compatible with oneChannelGUI |
| geoVSbioc | linking GEO platforms to available BioC annotations libraries |
| getNGSannotation | Retrieving genome annotation from ENSEMBL |
| GetNormalizationMethod | Starting oneChannelGUI package |
| GOenrichment | Searching for Gene Ontology enriched terms within a set of differentially expressed genes |
| goseqInterface | Starting oneChannelGUI package |
| GOstatsHelp | Starting oneChannelGUI package |
| hsfa | Human microRNA data set |
| importfusions | Starting oneChannelGUI package |
| 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 |
| isoDiff | TuxedoSuite |
| javaFolder | Starting oneChannelGUI package |
| largedatasetNorm | Starting oneChannelGUI package |
| libraryFilesDir | Starting oneChannelGUI package |
| limma2paired | graphical interface apply linear model to two sample groups with batch effect. |
| limmaExons | graphical interface to limma for alternative splicing detection |
| listFilter | Subsetting an expression set using a list of Affymetrix ids |
| log2Conversion | Starting oneChannelGUI package |
| makeBED15 | This function creates files in BED15 format to be loaded on the UCSC browser |
| makeGCcontent | Building a list of gene-level GC frequencies |
| makeGeneScaffold | Building a GRange object at chromosome level on UCSC genome data |
| makeSam | makeSam |
| 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 |
| meVDownload | Starting oneChannelGUI package |
| midasFilter | Starting oneChannelGUI package |
| miRNAbowtieRun | Primary mapping of short reads with Bowtie/Picard for miRNA |
| ML.edesign | The function creates an data frame containing the parameters useful for class prediction |
| mmfa | Mouse microRNA data set |
| mRNAbowtieRun | Primary mapping of short reads with Bowtie/Picard for mRNA-seq |
| mRNAmiRCor | Filtering by mean of correlation between expression data and miRNA expression changes |
| myExpresso | Running the affy expresso function with the widget |
| ncHs.data | Subset of genomic regions with ncRNA of Homo sapiens |
| ncMm.data | Subset of genomic regions with ncRNA of Mus musculus |
| ncRn.data | Subset of genomic regions with ncRNA in Rattus norvegicus |
| ncScaffold | stand alone function to generate a scaffold containing only ncRNA location from ENSEMBL |
| NewLimmaFile | Starting oneChannelGUI package |
| NewLimmaFileNGS | Starting oneChannelGUI package |
| ngsperlDownload | Starting oneChannelGUI package |
| NGSreformat | reformating output of NGS primary tools software |
| 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 |
| OpenmiRanalyserfiles | Starting oneChannelGUI package |
| OpenmiRBam | Starting oneChannelGUI package |
| OpenmiRExpress | Starting oneChannelGUI package |
| OpenmiRProfiles | Starting oneChannelGUI package |
| OpenmiRShrimp | Starting oneChannelGUI package |
| OpenmRNABam | This function loads Bam files generated by local mapping with bowte in oneChannelGUI |
| OpenNgsfiles | Starting oneChannelGUI package |
| openPdf | Starting oneChannelGUI package |
| pamrHelp | Starting oneChannelGUI package |
| pdmclassHelp | Starting oneChannelGUI package |
| plierToZero | Setting to 0 low log2 intensity values generated with plier |
| plotcoverage | Starting oneChannelGUI package |
| plotDE.exons | Starting oneChannelGUI package |
| 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 |
| qcMDS | This function plots the sample relations based on multidimensional scaling using the plotMDS.dge edgeR function |
| 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 |
| Reads2logos | Extracting info on the counts associated to a differentially expressed ncRNA gene |
| recoverUnfiltered | Starting oneChannelGUI package |
| refiningPeaks | This function refines the structure of the genomics peaks, checking for the presence nearby peaks that cna be combined |
| reformatGdl | This function reorganizes single NGS data in a matrix to be used for statistical analysis. |
| refseqDownload | Retrieving Reference Sequences from NCBI ftp |
| retrieveMirTargets | graphical interface to RmiR.Hs.miRNA library. |
| retrievePSRseq | This function, given a file containing exon-level probesets retrieves Probe selection Regions, PRS, from RRE db |
| retrievePSRseq1gid | This function, given a gene-level probeset id, retrieves Probe selection Regions, PRS, from RRE db |
| reviqrFilter | Reverse interquantile filtering with a mouse click |
| RmiRInterface | graphical interface to RmiR library. |
| rnfa | Rat microRNA data set |
| 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 |
| SaveLimmaFile | Starting oneChannelGUI package |
| setBinDir | 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 |
| standAloneAddingAnnotation | Attach to a data frame containing gene-level data derived from Affymetrix exon arrays the annotations derived by netaffx |
| standAloneBuildingLocalAnnotation | Creates a data frame with gene-level annotation data for exon arrays using the netaffx database |
| startmeV | 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) |
| tophat | TuxedoSuite |
| tophatrun | Starting oneChannelGUI package |
| topTable.exons | topTable.exons |
| topTable.genes | Starting oneChannelGUI package |
| trainTest | Creating a training set and a test set by a mouse click |
| tuxedoMenu | Starting oneChannelGUI package |
| tuxedoSetup | tuxedoSetup |
| 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 |
| wrapNGS | Downloading software for NGS |
| wrapScaffold | A wrapper for makeGCcontent, makeGeneScaffold |
| .annotation | Starting oneChannelGUI package |
| .myfindOverlaps | Starting oneChannelGUI package |
| .myrk | Starting oneChannelGUI package |