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

Documentation for package ‘oneChannelGUI’ version 1.22.12

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.
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
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
chooseEDir	Starting oneChannelGUI package
chooseInDir	TuxedoSuite
chooseOutDir	TuxedoSuite
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.
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
DESeqInterface	Starting oneChannelGUI package
dfMAplot	MA and Volcano plots from data present in a limma derived topTable

-- 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
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 --

filteringmiRtargets	Subsetting an expression set using a list of gene which are putative targets for a miRNA
filteringTable	Filtering a tab delimited file

-- 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 --

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
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
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

-- 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

-- P --

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

-- 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
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
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
trainTest	Creating a training set and a test set by a mouse click
tuxedoMenu	Starting oneChannelGUI package

-- 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
wrapScaffold	A wrapper for makeGCcontent, makeGeneScaffold

-- misc --

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