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

This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis

AuthorRaffale A Calogero, Bioinformatics and Genomics Unit, Molecular Biotechnology Center, Torino (Italy)
Date of publicationNone
MaintainerRaffaele A Calogero <raffaele.calogero@unito.it>
LicenseArtistic-2.0
Version1.40.0
http://www.bioinformatica.unito.it/oneChannelGUI/

View on Bioconductor

Man pages

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...

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...

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

Files in this package

oneChannelGUI/DESCRIPTION
oneChannelGUI/NAMESPACE
oneChannelGUI/NEWS
oneChannelGUI/R
oneChannelGUI/R/RNAseq.R oneChannelGUI/R/chimeraGUI.R oneChannelGUI/R/classificationmenu.R oneChannelGUI/R/dataminingmenu.R oneChannelGUI/R/dexseq.R
oneChannelGUI/R/exonmenu.R
oneChannelGUI/R/filemenu.R oneChannelGUI/R/filteringmenu.R oneChannelGUI/R/generaltoolsmenu.R oneChannelGUI/R/helpmenu.R oneChannelGUI/R/initialize.extAffylmGUI.R oneChannelGUI/R/modellingstatmenu.R oneChannelGUI/R/normalizemenu.R oneChannelGUI/R/oneChannelGUI.R oneChannelGUI/R/oneChannelGUI.start.R oneChannelGUI/R/permutationstatmenu.R
oneChannelGUI/R/qcmenu.R
oneChannelGUI/R/reformatmenu.R oneChannelGUI/R/standalonefunctions.R oneChannelGUI/R/targetmenu.R oneChannelGUI/R/tuxedo.R oneChannelGUI/R/zzz.R
oneChannelGUI/build
oneChannelGUI/build/vignette.rds
oneChannelGUI/data
oneChannelGUI/data/bofa.rda
oneChannelGUI/data/chrLength.rda
oneChannelGUI/data/geoVSbioc.rda
oneChannelGUI/data/hsfa.rda
oneChannelGUI/data/mmfa.rda
oneChannelGUI/data/ncHs.data.rda
oneChannelGUI/data/ncMm.data.rda
oneChannelGUI/data/ncRn.data.rda
oneChannelGUI/data/rnfa.rda
oneChannelGUI/inst
oneChannelGUI/inst/CITATION
oneChannelGUI/inst/batch
oneChannelGUI/inst/batch/batch_dexseq_exon.R
oneChannelGUI/inst/doc
oneChannelGUI/inst/doc/Exon-level.analysis.Rnw
oneChannelGUI/inst/doc/Exon-level.analysis.pdf
oneChannelGUI/inst/doc/RNAseq.Rnw
oneChannelGUI/inst/doc/RNAseq.pdf
oneChannelGUI/inst/doc/gene-level.analysis.Rnw
oneChannelGUI/inst/doc/gene-level.analysis.pdf
oneChannelGUI/inst/doc/install.R
oneChannelGUI/inst/doc/install.Rnw
oneChannelGUI/inst/doc/install.pdf
oneChannelGUI/inst/doc/standAloneFunctions.Rnw
oneChannelGUI/inst/doc/standAloneFunctions.pdf
oneChannelGUI/inst/etc
oneChannelGUI/inst/etc/affylmGUI-menus.affy.txt
oneChannelGUI/inst/etc/affylmGUI-menus.exon.txt
oneChannelGUI/inst/etc/affylmGUI-menus.gene.txt
oneChannelGUI/inst/etc/affylmGUI-menus.illumina.txt
oneChannelGUI/inst/etc/affylmGUI-menus.large.datasets.txt
oneChannelGUI/inst/etc/affylmGUI-menus.ngs.datasets.txt
oneChannelGUI/inst/etc/localData.txt
oneChannelGUI/inst/etc/netaffxUpdates.txt
oneChannelGUI/inst/perl_scripts
oneChannelGUI/inst/perl_scripts/Adapter_trimCRA.pl
oneChannelGUI/inst/perl_scripts/MicroRazerSENSEMBL2genominator.hs.pl
oneChannelGUI/inst/perl_scripts/README.txt
oneChannelGUI/inst/perl_scripts/bta_precursor.fa
oneChannelGUI/inst/perl_scripts/fastq_to_fasta.pl
oneChannelGUI/inst/perl_scripts/hsa_precursor.fa
oneChannelGUI/inst/perl_scripts/mmu_precursor.fa
oneChannelGUI/inst/perl_scripts/rno_precursor.fa
oneChannelGUI/inst/perl_scripts/shrimp2bed.mm.pl
oneChannelGUI/inst/perl_scripts/shrimpENSEMBL2genominator.hs.pl
oneChannelGUI/inst/perl_scripts/shrimpENSEMBL2genominator.mirbase.pl
oneChannelGUI/inst/perl_scripts/shrimpENSEMBL2genominator.mm.pl
oneChannelGUI/inst/perl_scripts/shrimpENSEMBL2genominator.nc.pl
oneChannelGUI/man
oneChannelGUI/man/AptMidas.Rd oneChannelGUI/man/EDANtFreq.Rd oneChannelGUI/man/EDAplotQuality.Rd oneChannelGUI/man/EDAreadNumber.Rd oneChannelGUI/man/EG2probeset.Rd oneChannelGUI/man/GOenrichment.Rd oneChannelGUI/man/IPAlistFilter.Rd oneChannelGUI/man/ML.edesign.Rd oneChannelGUI/man/NGSreformat.Rd
oneChannelGUI/man/OpenBeadStudioFiles.rd
oneChannelGUI/man/OpenLargefiles.Rd oneChannelGUI/man/OpenmRNABam.Rd oneChannelGUI/man/PlotOptionsv1.Rd oneChannelGUI/man/Reads2logos.Rd oneChannelGUI/man/RmiRInterface.Rd oneChannelGUI/man/VennDiagram.Rd oneChannelGUI/man/adaptorTrimm.Rd oneChannelGUI/man/annotateNGSeset.Rd oneChannelGUI/man/bayseqInterface.Rd oneChannelGUI/man/biomartFilter.Rd oneChannelGUI/man/bofa.Rd oneChannelGUI/man/bowtieBuilt.Rd oneChannelGUI/man/bowtieDownload.Rd oneChannelGUI/man/bowtieGenomes.Rd oneChannelGUI/man/buildingLocalAnnotation.Rd oneChannelGUI/man/chrLength.Rd oneChannelGUI/man/colExtract.Rd oneChannelGUI/man/combineGeoMSF.Rd oneChannelGUI/man/combining2eSet.Rd oneChannelGUI/man/consistentFilters.Rd oneChannelGUI/man/cosieWrapper.Rd oneChannelGUI/man/createGeoTarget.Rd oneChannelGUI/man/crosshybFilter.Rd oneChannelGUI/man/ctrtrtHeatmap.Rd oneChannelGUI/man/desGenes.Rd oneChannelGUI/man/dexCounts.Rd oneChannelGUI/man/dexExons.Rd oneChannelGUI/man/dfMAplot.Rd oneChannelGUI/man/eSet4meV.Rd oneChannelGUI/man/edgeRNorm.Rd oneChannelGUI/man/edgerInterface.Rd oneChannelGUI/man/erankProdAltSpl.Rd oneChannelGUI/man/erankProdAltSplFilterl.Rd oneChannelGUI/man/exonContrasts.Rd oneChannelGUI/man/exonScaffold.Rd oneChannelGUI/man/exonTopTableExtract.Rd oneChannelGUI/man/exonsSpecific2as.Rd oneChannelGUI/man/extractAffyids.Rd oneChannelGUI/man/extractmirTargets.Rd oneChannelGUI/man/filteringTable.Rd oneChannelGUI/man/filteringmiRtargets.Rd oneChannelGUI/man/geneExonLibs.Rd oneChannelGUI/man/genomePlot.Rd oneChannelGUI/man/genomeStudioReformat.Rd oneChannelGUI/man/geoVSbioc.Rd oneChannelGUI/man/getNGSannotation.Rd oneChannelGUI/man/hsfa.Rd oneChannelGUI/man/inspecting.one.splice.index.Rd oneChannelGUI/man/inspecting.splice.index.Rd oneChannelGUI/man/intensityFilter.Rd oneChannelGUI/man/iqrFilter.Rd oneChannelGUI/man/limma2paired.Rd oneChannelGUI/man/limmaExons.Rd oneChannelGUI/man/listFilter.Rd oneChannelGUI/man/mRNAbowtieRun.Rd oneChannelGUI/man/mRNAmiRCor.Rd oneChannelGUI/man/makeBED15.Rd oneChannelGUI/man/makeGCcontent.Rd oneChannelGUI/man/makeGeneScaffold.Rd oneChannelGUI/man/makeSam.Rd oneChannelGUI/man/mapping2RefSeq.Rd oneChannelGUI/man/mapping2ensembl.Rd oneChannelGUI/man/mapping2exon.Rd oneChannelGUI/man/masigpro.Rd oneChannelGUI/man/masigpro.edesign.Rd oneChannelGUI/man/masigpro.view.Rd oneChannelGUI/man/metaArrayIC.Rd
oneChannelGUI/man/metaArrayMerge.rd
oneChannelGUI/man/miRNAbowtieRun.Rd oneChannelGUI/man/mmfa.Rd oneChannelGUI/man/myExpresso.Rd oneChannelGUI/man/ncHs.data.Rd oneChannelGUI/man/ncMm.data.Rd oneChannelGUI/man/ncRn.data.Rd oneChannelGUI/man/ncScaffold.Rd oneChannelGUI/man/normBoxplot.Rd oneChannelGUI/man/ocPlotHist.Rd oneChannelGUI/man/ocPlotPCA.Rd oneChannelGUI/man/oneChannelGUI-package.Rd oneChannelGUI/man/oneChannelGUI.Rd oneChannelGUI/man/plierToZero.Rd oneChannelGUI/man/plotGO.Rd oneChannelGUI/man/plotVariantSI.Rd oneChannelGUI/man/qcMDS.Rd oneChannelGUI/man/rankProd.Rd oneChannelGUI/man/rankingConversion.Rd oneChannelGUI/man/rawBoxplotPN.Rd oneChannelGUI/man/rawpCheck.Rd oneChannelGUI/man/refiningPeaks.Rd oneChannelGUI/man/reformatGdl.Rd oneChannelGUI/man/refseqDownload.Rd oneChannelGUI/man/retrieveMirTargets.Rd oneChannelGUI/man/retrievePSRseq.Rd oneChannelGUI/man/retrievePSRseq1gid.Rd oneChannelGUI/man/reviqrFilter.Rd oneChannelGUI/man/rnfa.Rd oneChannelGUI/man/runningJetta.Rd oneChannelGUI/man/sample.size.evaluation.Rd oneChannelGUI/man/sample.size.evaluation1.Rd oneChannelGUI/man/showDataset.Rd oneChannelGUI/man/showTopTable.Rd oneChannelGUI/man/siggenes.Rd oneChannelGUI/man/simFilter.Rd oneChannelGUI/man/spliceIndex.Rd oneChannelGUI/man/standAloneAddingAnnotation.Rd oneChannelGUI/man/standAloneBuildingLocalAnnotation.Rd oneChannelGUI/man/targetWidget.Rd oneChannelGUI/man/templA.Rd oneChannelGUI/man/topTable.exons.Rd oneChannelGUI/man/tophat.Rd oneChannelGUI/man/trainTest.Rd oneChannelGUI/man/tuxedoSetup.Rd oneChannelGUI/man/updateLibs.Rd oneChannelGUI/man/variantExons.Rd oneChannelGUI/man/variantSI.Rd oneChannelGUI/man/wrapNGS.Rd oneChannelGUI/man/wrapScaffold.Rd
oneChannelGUI/vignettes
oneChannelGUI/vignettes/Exon-level.analysis.Rnw
oneChannelGUI/vignettes/RNAseq.Rnw
oneChannelGUI/vignettes/fig1.png
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oneChannelGUI/vignettes/fignew42.pdf
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oneChannelGUI/vignettes/gene-level.analysis.Rnw
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oneChannelGUI/vignettes/install.Rnw
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oneChannelGUI/vignettes/standAloneFunctions.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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