Man pages for Bioconductor-mirror/oneChannelGUI
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

adaptorTrimmTrimming 3,5 end primers for miRNAs NGS
annotateNGSesetAssociate annotation to NGS data loaded in oneChannelGUI
AptMidasGraphical interface to APT midas
bayseqInterfacegraphical interface to baySeq library.
biomartFilterFiltering only gene-level probe sets with multiple ensembl...
bofaBovine microRNA data set
bowtieBuiltDownloading Bowtie prebuilt reference sets
bowtieDownloadDownloading Bowtie and Picard tools
bowtieGenomesDownloading and building chromosome level genomes references...
buildingLocalAnnotationUpdates local gene-level annotation data for gene and exon...
chrLengthChromosomes lenghts
colExtractExtract a column from a tab delimited file with header
combineGeoMSFThis function allows to combine GEO Matrix Series Files...
combining2eSetThis function allows to combine two matrices extracted from...
consistentFiltersThis function allows filtering using the combination of...
cosieWrapperA wrapper to cosie, Corrected Splicing Indices for Exon...
createGeoTargetCreating a affylmGUI Target starting from a GEO Matrix series...
crosshybFilterRemoving from exon array gene/exon level probe sets...
ctrtrtHeatmapCreating heat map for maSigPro data with only one treatment...
desGenesdesGenes
dexCountsdexCounts
dexExonsdexExons
dfMAplotMA and Volcano plots from data present in a limma derived...
EDANtFreqPlotting Nts frequency for mapped reads extracted from BAM...
EDAplotQualityPlotting Quality scores for mapped reads extracted from BAM...
EDAreadNumberPlotting the number of mapped reads extracted from BAM files
edgerInterfacegraphical interface to edgeR library.
edgeRNormThis function scale-normalize NGS raw data as described by...
EG2probesetThis function allows to link GeneBank and Entrez Gene ids to...
erankProdAltSplImplementation of the Rank Product method for the detection...
erankProdAltSplFilterlFiltering Rank Product results for the detection of...
eSet4meVThis function allows to reformat an eSet to be loaded in meV...
exonContrastsDefining t-test regularized p-values
exonScaffoldstand alone function to generate a scaffold containing only...
exonsSpecific2asDefining the exons associated to the various alternative...
exonTopTableExtractExtracts data on the basis of a defined t-test regularized...
extractAffyidsExtracting probe ids associated to a specific Gene Ontology...
extractmirTargetsExtract miRNA targets showing a opposite regulation with...
filteringmiRtargetsSubsetting an expression set using a list of gene which are...
filteringTableFiltering a tab delimited file
geneExonLibsDownload the Library files for gene and exon analysis
genomePlotThis function plots average intensity signals for two group...
genomeStudioReformatThe present function reformat an expression file exported by...
geoVSbioclinking GEO platforms to available BioC annotations libraries
getNGSannotationRetrieving genome annotation from ENSEMBL
GOenrichmentSearching for Gene Ontology enriched terms within a set of...
hsfaHuman microRNA data set
inspecting.one.splice.indexPlotting on the profiles of splice indexes for a transcript...
inspecting.splice.indexPlotting on a pdf file the profiles of splice indexes
intensityFilterintensity filtering with a mouse click
IPAlistFilterFiltering an expression set using a set of Entrez genes...
iqrFilterInterquantile filtering with a mouse click
limma2pairedgraphical interface apply linear model to two sample groups...
limmaExonsgraphical interface to limma for alternative splicing...
listFilterSubsetting an expression set using a list of Affymetrix ids
makeBED15This function creates files in BED15 format to be loaded on...
makeGCcontentBuilding a list of gene-level GC frequencies
makeGeneScaffoldBuilding a GRange object at chromosome level on UCSC genome...
makeSammakeSam
mapping2ensemblAssociating e-level probe sets to entrez gene exonic...
mapping2exonThis function maps on exon-level Probe Selection Region (PSR)...
mapping2RefSeqThis function maps on NCBI Reference sequences spliced exons...
masigproThe function executes maSigPro analysis
masigpro.edesignThe function creates an edesign object needed to run maSigPro
masigpro.viewThe function allows the visualization of maSigPro results
metaArrayICGraphical interface to metaArray Integrative Correlation...
metaArrayMergeTool to create a merge object for metaArray package
miRNAbowtieRunPrimary mapping of short reads with Bowtie/Picard for miRNA
ML.edesignThe function creates an data frame containing the parameters...
mmfaMouse microRNA data set
mRNAbowtieRunPrimary mapping of short reads with Bowtie/Picard for...
mRNAmiRCorFiltering by mean of correlation between expression data and...
myExpressoRunning the affy expresso function with the widget
ncHs.dataSubset of genomic regions with ncRNA of Homo sapiens
ncMm.dataSubset of genomic regions with ncRNA of Mus musculus
ncRn.dataSubset of genomic regions with ncRNA in Rattus norvegicus
ncScaffoldstand alone function to generate a scaffold containing only...
NGSreformatreformating output of NGS primary tools software
normBoxplotBox plot of the arrays data available in NormalizeAffyData...
ocPlotHistGene/Exon level density plots
ocPlotPCAGene/Exon level density plots
oneChannelGUIStarting oneChannelGUI package
oneChannelGUI-packageSet of functions extending the capability of affylmGUI...
OpenBeadStudioFilesRead BeadStudio expression data file
OpenLargefilesThis function loads large data set made from tab delimited...
OpenmRNABamThis function loads Bam files generated by local mapping with...
plierToZeroSetting to 0 low log2 intensity values generated with plier
plotGOPlotting parents of a GO term with few mouse click
PlotOptionsv1A modified version of the function used in affyPLM library
plotVariantSIThis function plots on UCSC genome browser data derived by...
qcMDSThis function plots the sample relations based on...
rankingConversionThis function transforms intensity data in normalized ranks
rankProdgraphical interface to rank product method implemented in...
rawBoxplotPNPlotting raw log2 intensities from controls
rawpCheckRaw p-value distribution from limma analysis by a mouse click
Reads2logosExtracting info on the counts associated to a differentially...
refiningPeaksThis function refines the structure of the genomics peaks,...
reformatGdlThis function reorganizes single NGS data in a matrix to be...
refseqDownloadRetrieving Reference Sequences from NCBI ftp
retrieveMirTargetsgraphical interface to RmiR.Hs.miRNA library.
retrievePSRseqThis function, given a file containing exon-level probesets...
retrievePSRseq1gidThis function, given a gene-level probeset id, retrieves...
reviqrFilterReverse interquantile filtering with a mouse click
RmiRInterfacegraphical interface to RmiR library.
rnfaRat microRNA data set
runningJettagraphical interface to MADS/jetta R library.
sample.size.evaluationThe function executes and plots results from ssize and delta...
sample.size.evaluation1The function executes functions from the sizepower packahe
showDatasetGrabbing info about the available expression set
showTopTableModification of the function immplemented in affylmGUI to...
siggenesThe function executes SAM analysis implemented in siggenes...
simFilterThis function allows filtering on the basis of the average...
spliceIndexThis function coverts the exon intenisty data in a slice...
standAloneAddingAnnotationAttach to a data frame containing gene-level data derived...
standAloneBuildingLocalAnnotationCreates a data frame with gene-level annotation data for exon...
targetWidgetWidget to create a target file to load .CEL files
templAGenerating a template A to be uploaded in Ingenuity Pathways...
tophatTuxedoSuite
topTable.exonstopTable.exons
trainTestCreating a training set and a test set by a mouse click
tuxedoSetuptuxedoSetup
updateLibsThis function allows to update the present installation of...
variantExonsThis function is used to generate a table containing...
variantSIThis function allows filtering on the basis of variant exons
VennDiagramVenn diagrams using two or three lists
wrapNGSDownloading software for NGS
wrapScaffoldA wrapper for makeGCcontent, makeGeneScaffold
Bioconductor-mirror/oneChannelGUI documentation built on July 28, 2017, 5:23 a.m.