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

aggregateTagClustersAggregate TCs across all samples
annotateCTSSAnnotate and compute summary statistics
bam2CTSSbam2CTSS
byCtssApply functions to identical CTSSes.
CAGEexp-classCAGEr class to hold all data and metadata about one CAGE...
CAGEr-classCAGEr objects
CAGEr_MulticoreMulticore support in CAGEr
CAGEr-packageAnalysis of CAGE (Cap Analysis of Gene Expression) sequencing...
CAGEset-classClass '"CAGEset"'
clusterAggregateAndSumAggregate identical clusters and sum their scores.
clusterCTSSCluster CTSSs into tag clusters
coerceInBSgenomecoerceInBSgenome
consensusClusterConvertorsPrivate functions to convert CC formats
consensusClustersGet or set consensus clusters from CAGEr objects
consensusClustersDESeq2Export _consensus cluster_ expression data for DESeq2...
consensusClustersQuantileQuantile metadata stored in CAGEr objects.
consensusClustersTpmExtracting consensus clusters tpm matrix from CAGEset object
coverage-functionsPrivate functions behind 'cumulativeCTSSdistribution'
CTSS-classClasses for type safety.
CTSSclusteringMethodGet /set CTSS clustering method
CTSScoordinatesGenomic coordinates of TSSs from a 'CAGEr' object
CTSScumulativesTagClustersGet/set CTSS cumulative TC or CC data
CTSSnormalizedTpmExtracting normalized CAGE signal for TSSs from CAGEr objects
CTSStagCountExtract raw CAGE TSSs expression tables from 'CAGEr' objects
CTSStagCountTableExtracting CAGE tag count for TSSs from CAGEr objects
CTSStoGenesMake a gene expression table.
cumulativeCTSSdistributionCumulative sums of CAGE counts along genomic regions
CustomConsensusClustersExpression levels of consensus cluster
distclu-functionsPrivate functions for distance clustering.
exampleCAGEexpExample CAGEexp object.
exampleCAGEsetExample CAGEset object with zebrafish CAGE data
exampleZv9_annotExample zebrafish annotation data
exportCTSStoBedGraphCreating bedGraph/bigWig tracks of CAGE transcription starts...
exportToBedCreate BED tracks of TSSs and clusters of TSSs
expressionClassesExtract labels of expression classes
extractExpressionClassExtract elements of the specified expression class
FANTOM5humanSamplesList of FANTOM5 human CAGE samples
FANTOM5mouseSamplesList of FANTOM5 mouse CAGE samples
GeneExpDESeq2Export gene expression data for DESeq2 analysis
GeneExpSERetreives the SummarizedExperiment containing gene expression...
genomeNameExtracting genome name from CAGEr objects
getCTSSReading CAGE data from input file(s) and detecting TSSs
getExpressionProfilesCAGE data based expression clustering
getShiftingPromotersSelect consensus clusters with shifting score above threshold
hanabiCalcultate richness in preparation for plotting
hanabi-classHanabi class
hanabiPlothanabiPlot
import.bamimport.bam
import.bam.ctssimport.bam.ctss
import.bedCTSSimport.bedCTSS
import.bedmoleculeimport.bedmolecule
import.bedScoreimport.bedScore
import.CAGEscanMoleculeimport.CAGEscanMolecule
import.CTSSimport.CTSS
importPublicDataImporting publicly available CAGE data from various resources
inputFilesExtracting paths to input files from CAGEr objects
inputFilesTypeInput file formats for CAGEr objects
librarySizesExtracting library sizes from CAGEr objects
loadFileIntoGPosloadFileIntoGPos
mapStatsProcess mapping statistics
mapStatsScopesmapStats scopes
mergeCAGEsetsMerge two CAGEr objects into one
mergeSamplesMerge CAGE samples
moleculesGR2CTSSmoleculesGR2CTSS
normalizeTagCountNormalizing raw CAGE tag count
parseCAGEscanBlocksToGrangeTSSparseCAGEscanBlocksToGrangeTSS
plotAnnotPlot annotation statistics
plotCorrelationPairwise scatter plots and correlations of CAGE signal
plotExpressionProfilesPlotting expression profiles derived from CAGE data
plot.hanabiPlotting Hanabi objects
plotInterquantileWidthPlot cluster widths
plotReverseCumulativesPlot reverse cumulative number of CAGE tags per CTSS
powerLaw.powerLaw
quantilePositionsDetermine CTSS quantile positions within clusters
QuantileWidthFunctionsGet quantile positions
ranges2annothierarchical annotation of CTSSes
ranges2genesranges2genes
ranges2namesranges2names
sampleLabelsGet and set sample labels
scoreShiftCalculate promoter shifting score
seqNameTotalsSERetreives the SummarizedExperiment containing chromosome...
setColorsSet colors for samples
show-methodsMethods for function 'show'
strandInvadersDetect and remove strand invasion artefacts
summariseChrExprExpression levels by chromosomes
tagClusterConvertorsPrivate functions to convert TC formats
tagClustersExtract tag clusters (TCs) for individual CAGE experiments
tagClustersQuantileQuantile metadata stored in CAGEr objects.
CAGEr documentation built on June 30, 2018, 6 p.m.