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

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Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

Author
Vanja Haberle, Department of Biology, University of Bergen, Norway <vanja.haberle@gmail.com>
Date of publication
None
Maintainer
Vanja Haberle <vanja.haberle@gmail.com>
License
GPL-3
Version
1.16.0

View on Bioconductor

Man pages

aggregateTagClusters
Aggregating tag clusters across multiple CAGE datasets
CAGEr-package
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing...
CAGEset-class
Class '"CAGEset"'
clusterCTSS
Clustering CTSSs into tag clusters (TCs)
consensusClusters
Extracting consensus clusters from CAGEset object
consensusClustersTpm
Extracting consensus clusters tpm matrix from CAGEset object
CTSSclusteringMethod
Extracting CTSS clustering method from CAGEset object
CTSScoordinates
Extracting genomic coordinates of TSSs from CAGEset object
CTSSnormalizedTpm
Extracting normalized CAGE signal for TSSs from CAGEset...
CTSStagCount
Extracting CAGE tag count for TSSs from CAGEset object
cumulativeCTSSdistribution
Calculating cumulative sum of CAGE signal along genomic...
exampleCAGEset
Example CAGEset object with zebrafish CAGE data
exportCTSStoBedGraph
Creating bedGraph/bigWig tracks of CAGE transcription starts...
exportToBed
Creating BED tracks of TSSs and clusters of TSSs
expressionClasses
Extracting labels of expression classes
extractExpressionClass
Extracting elements of the specified expression class
FANTOM5humanSamples
List of FANTOM5 human CAGE samples
FANTOM5mouseSamples
List of FANTOM5 mouse CAGE samples
genomeName
Extracting genome name from CAGEset object
getCTSS
Reading CAGE data from input file(s) and detecting TSSs
getExpressionProfiles
CAGE data based expression clustering
getShiftingPromoters
Selecting consensus clusters with shifting score above...
importPublicData
Importing publicly available CAGE data from various resources
inputFiles
Extracting paths to input files from CAGEset object
inputFilesType
Extracting type of input files from CAGEset object
librarySizes
Extracting library sizes from CAGEset object
mergeCAGEsets
Merging two CAGEset objects into one
mergeSamples
Merging CAGE datasets (samples)
normalizeTagCount
Normalizing raw CAGE tag count
plotCorrelation
Plotting pairwise scatter plots of CAGE signal and...
plotExpressionProfiles
Plotting expression profiles derived from CAGE data
plotInterquantileWidth
Plotting distribution of interquantile width
plotReverseCumulatives
Plotting reverse cumulative number of CAGE tags per CTSS
quantilePositions
Determining positions of CAGE signal quantiles within genomic...
sampleLabels
Extracting CAGE datasets labels from CAGEset object
scoreShift
Calculating promoter shifting score
setColors
Setting colors for samples
show-methods
Methods for function 'show'
tagClusters
Extracting tag clusters (TCs) for individual CAGE experiment...

Files in this package

CAGEr/DESCRIPTION
CAGEr/NAMESPACE
CAGEr/NEWS
CAGEr/R
CAGEr/R/AggregationFunctions.R
CAGEr/R/AggregationMethods.R
CAGEr/R/AllClasses.R
CAGEr/R/ClusteringFunctions.R
CAGEr/R/ClusteringMethods.R
CAGEr/R/CorrelationMethods.R
CAGEr/R/CumulativeDistributionFunctions.R
CAGEr/R/CumulativeDistributionMethods.R
CAGEr/R/ExportFunctions.R
CAGEr/R/ExportMethods.R
CAGEr/R/ExpressionProfilingMethods.R
CAGEr/R/GetMethods.R
CAGEr/R/ImportFunctions.R
CAGEr/R/ImportMethods.R
CAGEr/R/MergingMethods.R
CAGEr/R/NormalizationFunctions.R
CAGEr/R/NormalizationMethods.R
CAGEr/R/QuantileWidthFunctions.R
CAGEr/R/QuantileWidthMethods.R
CAGEr/R/ShiftingFunctions.R
CAGEr/R/ShiftingMethods.R
CAGEr/build
CAGEr/build/vignette.rds
CAGEr/data
CAGEr/data/FANTOM5humanSamples.RData
CAGEr/data/FANTOM5mouseSamples.RData
CAGEr/data/exampleCAGEset.RData
CAGEr/inst
CAGEr/inst/CITATION
CAGEr/inst/doc
CAGEr/inst/doc/CAGEr.R
CAGEr/inst/doc/CAGEr.Rnw
CAGEr/inst/doc/CAGEr.pdf
CAGEr/inst/extdata
CAGEr/inst/extdata/Zf.30p.dome.chr17.ctss
CAGEr/inst/extdata/Zf.high.chr17.ctss
CAGEr/inst/extdata/Zf.prim6.rep1.chr17.ctss
CAGEr/inst/extdata/Zf.prim6.rep2.chr17.ctss
CAGEr/inst/extdata/Zf.unfertilized.egg.chr17.ctss
CAGEr/man
CAGEr/man/CAGEr-package.Rd
CAGEr/man/CAGEset-class.Rd
CAGEr/man/CTSSclusteringMethod.Rd
CAGEr/man/CTSScoordinates.Rd
CAGEr/man/CTSSnormalizedTpm.Rd
CAGEr/man/CTSStagCount.Rd
CAGEr/man/FANTOM5humanSamples.Rd
CAGEr/man/FANTOM5mouseSamples.Rd
CAGEr/man/aggregateTagClusters.Rd
CAGEr/man/clusterCTSS.Rd
CAGEr/man/consensusClusters.Rd
CAGEr/man/consensusClustersTpm.Rd
CAGEr/man/cumulativeCTSSdistribution.Rd
CAGEr/man/exampleCAGEset.Rd
CAGEr/man/exportCTSStoBedGraph.Rd
CAGEr/man/exportToBed.Rd
CAGEr/man/expressionClasses.Rd
CAGEr/man/extractExpressionClass.Rd
CAGEr/man/genomeName.Rd
CAGEr/man/getCTSS.Rd
CAGEr/man/getExpressionProfiles.Rd
CAGEr/man/getShiftingPromoters.Rd
CAGEr/man/importPublicData.Rd
CAGEr/man/inputFiles.Rd
CAGEr/man/inputFilesType.Rd
CAGEr/man/librarySizes.Rd
CAGEr/man/mergeCAGEsets.Rd
CAGEr/man/mergeSamples.Rd
CAGEr/man/normalizeTagCount.Rd
CAGEr/man/plotCorrelation.Rd
CAGEr/man/plotExpressionProfiles.Rd
CAGEr/man/plotInterquantileWidth.Rd
CAGEr/man/plotReverseCumulatives.Rd
CAGEr/man/quantilePositions.Rd
CAGEr/man/sampleLabels.Rd
CAGEr/man/scoreShift.Rd
CAGEr/man/setColors.Rd
CAGEr/man/show-methods.Rd
CAGEr/man/tagClusters.Rd
CAGEr/vignettes
CAGEr/vignettes/CAGEr.Rnw
CAGEr/vignettes/CAGEr.bib
CAGEr/vignettes/images
CAGEr/vignettes/images/CAGEprotocol.pdf
CAGEr/vignettes/images/CTSS_reverse_cumulatives_all_samples.pdf
CAGEr/vignettes/images/CTSSbedGraph.pdf
CAGEr/vignettes/images/ConsensusClustersBed.pdf
CAGEr/vignettes/images/ConsensusClustersExpressionProfiles.pdf
CAGEr/vignettes/images/CumulativeDistributionAndQuantiles.pdf
CAGEr/vignettes/images/Pairwise_tag_count_correlation.jpg
CAGEr/vignettes/images/ShiftingPromoter.pdf
CAGEr/vignettes/images/ShiftingScore.pdf
CAGEr/vignettes/images/TagClustersBed.pdf
CAGEr/vignettes/images/TagClustersInterquantileWidth.pdf