| adaptorTrimm | Trimming 3,5 end primers for miRNAs NGS |
| annotateNGSeset | Associate annotation to NGS data loaded in oneChannelGUI |
| AptMidas | Graphical interface to APT midas |
| bayseqInterface | graphical interface to baySeq library. |
| biomartFilter | Filtering only gene-level probe sets with multiple ensembl... |
| 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... |
| buildingLocalAnnotation | Updates local gene-level annotation data for gene and exon... |
| chrLength | Chromosomes lenghts |
| colExtract | Extract a column from a tab delimited file with header |
| combineGeoMSF | This function allows to combine GEO Matrix Series Files... |
| combining2eSet | This function allows to combine two matrices extracted from... |
| consistentFilters | This function allows filtering using the combination of... |
| cosieWrapper | A wrapper to cosie, Corrected Splicing Indices for Exon... |
| createGeoTarget | Creating a affylmGUI Target starting from a GEO Matrix series... |
| crosshybFilter | Removing from exon array gene/exon level probe sets... |
| ctrtrtHeatmap | Creating heat map for maSigPro data with only one treatment... |
| desGenes | desGenes |
| dexCounts | dexCounts |
| dexExons | dexExons |
| dfMAplot | MA and Volcano plots from data present in a limma derived... |
| EDANtFreq | Plotting Nts frequency for mapped reads extracted from BAM... |
| EDAplotQuality | Plotting Quality scores for mapped reads extracted from BAM... |
| EDAreadNumber | Plotting the number of mapped reads extracted from BAM files |
| edgerInterface | graphical interface to edgeR library. |
| edgeRNorm | This function scale-normalize NGS raw data as described by... |
| EG2probeset | This function allows to link GeneBank and Entrez Gene ids to... |
| erankProdAltSpl | Implementation of the Rank Product method for the detection... |
| erankProdAltSplFilterl | Filtering Rank Product results for the detection of... |
| eSet4meV | This function allows to reformat an eSet to be loaded in meV... |
| exonContrasts | Defining t-test regularized p-values |
| exonScaffold | stand alone function to generate a scaffold containing only... |
| exonsSpecific2as | Defining the exons associated to the various alternative... |
| exonTopTableExtract | Extracts data on the basis of a defined t-test regularized... |
| extractAffyids | Extracting probe ids associated to a specific Gene Ontology... |
| extractmirTargets | Extract miRNA targets showing a opposite regulation with... |
| filteringmiRtargets | Subsetting an expression set using a list of gene which are... |
| filteringTable | Filtering a tab delimited file |
| geneExonLibs | Download the Library files for gene and exon analysis |
| genomePlot | This function plots average intensity signals for two group... |
| genomeStudioReformat | The present function reformat an expression file exported by... |
| geoVSbioc | linking GEO platforms to available BioC annotations libraries |
| getNGSannotation | Retrieving genome annotation from ENSEMBL |
| GOenrichment | Searching for Gene Ontology enriched terms within a set of... |
| hsfa | Human microRNA data set |
| inspecting.one.splice.index | Plotting on the profiles of splice indexes for a transcript... |
| inspecting.splice.index | Plotting on a pdf file the profiles of splice indexes |
| intensityFilter | intensity filtering with a mouse click |
| IPAlistFilter | Filtering an expression set using a set of Entrez genes... |
| iqrFilter | Interquantile filtering with a mouse click |
| limma2paired | graphical interface apply linear model to two sample groups... |
| limmaExons | graphical interface to limma for alternative splicing... |
| listFilter | Subsetting an expression set using a list of Affymetrix ids |
| makeBED15 | This function creates files in BED15 format to be loaded on... |
| makeGCcontent | Building a list of gene-level GC frequencies |
| makeGeneScaffold | Building a GRange object at chromosome level on UCSC genome... |
| makeSam | makeSam |
| mapping2ensembl | Associating e-level probe sets to entrez gene exonic... |
| mapping2exon | This function maps on exon-level Probe Selection Region (PSR)... |
| mapping2RefSeq | This function maps on NCBI Reference sequences spliced exons... |
| 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... |
| metaArrayMerge | Tool to create a merge object for metaArray package |
| miRNAbowtieRun | Primary mapping of short reads with Bowtie/Picard for miRNA |
| ML.edesign | The function creates an data frame containing the parameters... |
| mmfa | Mouse microRNA data set |
| mRNAbowtieRun | Primary mapping of short reads with Bowtie/Picard for... |
| mRNAmiRCor | Filtering by mean of correlation between expression data and... |
| 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... |
| NGSreformat | reformating output of NGS primary tools software |
| normBoxplot | Box plot of the arrays data available in NormalizeAffyData... |
| ocPlotHist | Gene/Exon level density plots |
| ocPlotPCA | Gene/Exon level density plots |
| oneChannelGUI | Starting oneChannelGUI package |
| oneChannelGUI-package | Set of functions extending the capability of affylmGUI... |
| OpenBeadStudioFiles | Read BeadStudio expression data file |
| OpenLargefiles | This function loads large data set made from tab delimited... |
| OpenmRNABam | This function loads Bam files generated by local mapping with... |
| 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... |
| qcMDS | This function plots the sample relations based on... |
| rankingConversion | This function transforms intensity data in normalized ranks |
| rankProd | graphical interface to rank product method implemented in... |
| 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... |
| refiningPeaks | This function refines the structure of the genomics peaks,... |
| reformatGdl | This function reorganizes single NGS data in a matrix to be... |
| 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... |
| retrievePSRseq1gid | This function, given a gene-level probeset id, retrieves... |
| 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... |
| 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... |
| siggenes | The function executes SAM analysis implemented in siggenes... |
| simFilter | This function allows filtering on the basis of the average... |
| spliceIndex | This function coverts the exon intenisty data in a slice... |
| standAloneAddingAnnotation | Attach to a data frame containing gene-level data derived... |
| standAloneBuildingLocalAnnotation | Creates a data frame with gene-level annotation data for exon... |
| targetWidget | Widget to create a target file to load .CEL files |
| templA | Generating a template A to be uploaded in Ingenuity Pathways... |
| tophat | TuxedoSuite |
| topTable.exons | topTable.exons |
| 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... |
| variantExons | This function is used to generate a table containing... |
| variantSI | This function allows filtering on the basis of variant exons |
| VennDiagram | Venn diagrams using two or three lists |
| wrapNGS | Downloading software for NGS |
| wrapScaffold | A wrapper for makeGCcontent, makeGeneScaffold |
