AptMidas                Graphical interface to APT midas
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
EG2probeset             This function allows to link GeneBank and
                        Entrez Gene ids to gene-level probe set ids
GOenrichment            Searching for Gene Ontology enriched terms
                        within a set of differentially expressed genes
IPAlistFilter           Filtering an expression set using a set of
                        Entrez genes extracted from Ingenuity Pathways
                        analysis (IPA)
ML.edesign              The function creates an data frame containing
                        the parameters useful for class prediction
NGSreformat             reformating output of NGS primary tools
                        software
OpenBeadStudioFiles     Read BeadStudio expression data file
OpenLargefiles          This function loads large data set made from
                        tab delimited files
OpenmRNABam             This function loads Bam files generated by
                        local mapping with bowte in oneChannelGUI
PlotOptionsv1           A modified version of the function used in
                        affyPLM library
Reads2logos             Extracting info on the counts associated to a
                        differentially expressed ncRNA gene
RmiRInterface           graphical interface to RmiR library.
VennDiagram             Venn diagrams using two or three lists
adaptorTrimm            Trimming 3,5 end primers for miRNAs NGS
annotateNGSeset         Associate annotation to NGS data loaded in
                        oneChannelGUI
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
chrLength               Chromosomes lenghts
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.
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
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
desGenes                desGenes
dexCounts               dexCounts
dexExons                dexExons
dfMAplot                MA and Volcano plots from data present in a
                        limma derived topTable
eSet4meV                This function allows to reformat an eSet to be
                        loaded in meV visualization software
edgeRNorm               This function scale-normalize NGS raw data as
                        described by Robinson and Oshlack Genome
                        Biology 2010, 11:R25
edgerInterface          graphical interface to edgeR library.
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
exonScaffold            stand alone function to generate a scaffold
                        containing only exon location from ENSEMBL
exonTopTableExtract     Extracts data on the basis of a defined t-test
                        regularized p-value
exonsSpecific2as        Defining the exons associated to the various
                        alternative isoforms
extractAffyids          Extracting probe ids associated to a specific
                        Gene Ontology term
extractmirTargets       Extract miRNA targets showing a opposite
                        regulation with respect to miRNA
filteringTable          Filtering a tab delimited file
filteringmiRtargets     Subsetting an expression set using a list of
                        gene which are putative targets for a miRNA
geneExonLibs            Download the Library files for gene and exon
                        analysis
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
goseqInterface          Starting oneChannelGUI package
hsfa                    Human microRNA data set
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
iqrFilter               Interquantile filtering with a mouse click
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
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
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
mapping2RefSeq          This function maps on NCBI Reference sequences
                        spliced exons detected by the function
                        oneChannelGUI: Inspecting splice indexes
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
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
metaArrayIC             Graphical interface to metaArray Integrative
                        Correlation function
metaArrayMerge          Tool to create a merge object for metaArray
                        package
miRNAbowtieRun          Primary mapping of short reads with
                        Bowtie/Picard for miRNA
mmfa                    Mouse microRNA data set
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
normBoxplot             Box plot of the arrays data available in
                        NormalizeAffyData slot
ocPlotHist              Gene/Exon level density plots
ocPlotPCA               Gene/Exon level density plots
oneChannelGUI-package   Set of functions extending the capability of
                        affylmGUI package
plierToZero             Setting to 0 low log2 intensity values
                        generated with plier
plotGO                  Plotting parents of a GO term with few mouse
                        click
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
rankProd                graphical interface to rank product method
                        implemented in RankProd Bioconductor library.
rankingConversion       This function transforms intensity data in
                        normalized ranks
rawBoxplotPN            Plotting raw log2 intensities from controls
rawpCheck               Raw p-value distribution from limma analysis by
                        a mouse click
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
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
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
simFilter               This function allows filtering on the basis of
                        the average splice index mean or min difference
                        between two groups
spliceIndex             This function coverts the exon intenisty data
                        in a slice index
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
targetWidget            Widget to create a target file to load .CEL
                        files
templA                  Generating a template A to be uploaded in
                        Ingenuity Pathways analysis (IPA)
topTable.exons          topTable.exons
tophat                  TuxedoSuite
trainTest               Creating a training set and a test set by a
                        mouse click
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
wrapNGS                 Downloading software for NGS
wrapScaffold            A wrapper for makeGCcontent, makeGeneScaffold
