Man pages for CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

aggregateTagClustersAggregating tag clusters across multiple CAGE datasets
CAGEr-packageAnalysis of CAGE (Cap Analysis of Gene Expression) sequencing...
CAGEset-classClass '"CAGEset"'
clusterCTSSClustering CTSSs into tag clusters (TCs)
consensusClustersExtracting consensus clusters from CAGEset object
consensusClustersTpmExtracting consensus clusters tpm matrix from CAGEset object
CTSSclusteringMethodExtracting CTSS clustering method from CAGEset object
CTSScoordinatesExtracting genomic coordinates of TSSs from CAGEset object
CTSSnormalizedTpmExtracting normalized CAGE signal for TSSs from CAGEset...
CTSStagCountExtracting CAGE tag count for TSSs from CAGEset object
cumulativeCTSSdistributionCalculating cumulative sum of CAGE signal along genomic...
exampleCAGEsetExample CAGEset object with zebrafish CAGE data
exportCTSStoBedGraphCreating bedGraph/bigWig tracks of CAGE transcription starts...
exportToBedCreating BED tracks of TSSs and clusters of TSSs
expressionClassesExtracting labels of expression classes
extractExpressionClassExtracting elements of the specified expression class
FANTOM5humanSamplesList of FANTOM5 human CAGE samples
FANTOM5mouseSamplesList of FANTOM5 mouse CAGE samples
genomeNameExtracting genome name from CAGEset object
getCTSSReading CAGE data from input file(s) and detecting TSSs
getExpressionProfilesCAGE data based expression clustering
getShiftingPromotersSelecting consensus clusters with shifting score above...
importPublicDataImporting publicly available CAGE data from various resources
inputFilesExtracting paths to input files from CAGEset object
inputFilesTypeExtracting type of input files from CAGEset object
librarySizesExtracting library sizes from CAGEset object
mergeCAGEsetsMerging two CAGEset objects into one
mergeSamplesMerging CAGE datasets (samples)
normalizeTagCountNormalizing raw CAGE tag count
plotCorrelationPlotting pairwise scatter plots of CAGE signal and...
plotExpressionProfilesPlotting expression profiles derived from CAGE data
plotInterquantileWidthPlotting distribution of interquantile width
plotReverseCumulativesPlotting reverse cumulative number of CAGE tags per CTSS
quantilePositionsDetermining positions of CAGE signal quantiles within genomic...
sampleLabelsExtracting CAGE datasets labels from CAGEset object
scoreShiftCalculating promoter shifting score
setColorsSetting colors for samples
show-methodsMethods for function 'show'
tagClustersExtracting tag clusters (TCs) for individual CAGE experiment...
CAGEr documentation built on Nov. 17, 2017, 11:34 a.m.