# A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

## Documentation for package ‘oneChannelGUI’ version 1.34.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

## -- A --

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

## -- B --

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

## -- C --

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

## -- D --

dabgFilter | Starting oneChannelGUI package
delete.ML | Starting oneChannelGUI package
deleteLocalData | Starting oneChannelGUI package
desCounts | Starting oneChannelGUI package
deseq2Processing | 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
downloadShrimp | Starting oneChannelGUI package

## -- E --

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
enrich | Starting oneChannelGUI package
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

## -- F --

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

## -- G --

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

## -- H --

hsfa | Human microRNA data set

## -- I --

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

## -- J --

javaFolder | Starting oneChannelGUI package

## -- L --

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
loadmirnapath | Starting oneChannelGUI package
log2Conversion | Starting oneChannelGUI package

## -- M --

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
miRNAde | Starting oneChannelGUI package
mirnaTable | Starting oneChannelGUI package
mirPath | Starting oneChannelGUI package
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

## -- N --

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

## -- O --

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

## -- P --

pamrHelp | Starting oneChannelGUI package
pdmclassHelp | Starting oneChannelGUI package
permuting | 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

## -- Q --

qcMDS | This function plots the sample relations based on multidimensional scaling using the plotMDS.dge edgeR function

## -- R --

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
runEnrichment | Starting oneChannelGUI package
runningJetta | graphical interface to MADS/jetta R library.

## -- S --

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

## -- T --

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

## -- U --

updateLibs | This function allows to update the present installation of Bioconductor

## -- V --

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

## -- W --

whichKindOfArray | Starting oneChannelGUI package
wrapNGS | Downloading software for NGS
wrapperMirnaCounts | Starting oneChannelGUI package
wrapScaffold | A wrapper for makeGCcontent, makeGeneScaffold

## -- misc --

.annotation | Starting oneChannelGUI package
.myfindOverlaps | Starting oneChannelGUI package
.myrk | Starting oneChannelGUI package