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

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

AuthorVanja Haberle, Department of Biology, University of Bergen, Norway <vanja.haberle@gmail.com>
Date of publicationNone
MaintainerVanja Haberle <vanja.haberle@gmail.com>
LicenseGPL-3
Version1.16.0

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...

Functions

aggregateTagClusters Man page
aggregateTagClusters,CAGEset-method Man page
CAGEr Man page
CAGEr-package Man page
CAGEset Man page
CAGEset-class Man page
clusterCTSS Man page
clusterCTSS,CAGEset-method Man page
coerce,data.frame,CAGEset-method Man page
consensusClusters Man page
consensusClusters,CAGEset-method Man page
consensusClustersTpm Man page
consensusClustersTpm,CAGEset-method Man page
CTSSclusteringMethod Man page
CTSSclusteringMethod,CAGEset-method Man page
CTSScoordinates Man page
CTSScoordinates,CAGEset-method Man page
CTSSnormalizedTpm Man page
CTSSnormalizedTpm,CAGEset-method Man page
CTSStagCount Man page
CTSStagCount,CAGEset-method Man page
cumulativeCTSSdistribution Man page
cumulativeCTSSdistribution,CAGEset-method Man page
exampleCAGEset Man page
exportCTSStoBedGraph Man page
exportCTSStoBedGraph,CAGEset-method Man page
exportToBed Man page
exportToBed,CAGEset-method Man page
expressionClasses Man page
expressionClasses,CAGEset-method Man page
extractExpressionClass Man page
extractExpressionClass,CAGEset-method Man page
FANTOM5humanSamples Man page
FANTOM5mouseSamples Man page
genomeName Man page
genomeName,CAGEset-method Man page
getCTSS Man page
getCTSS,CAGEset-method Man page
getExpressionProfiles Man page
getExpressionProfiles,CAGEset-method Man page
getShiftingPromoters Man page
getShiftingPromoters,CAGEset-method Man page
importPublicData Man page
importPublicData,character,character,ANY,character-method Man page
inputFiles Man page
inputFiles,CAGEset-method Man page
inputFilesType Man page
inputFilesType,CAGEset-method Man page
librarySizes Man page
librarySizes,CAGEset-method Man page
mergeCAGEsets Man page
mergeCAGEsets,CAGEset,CAGEset-method Man page
mergeSamples Man page
mergeSamples,CAGEset,numeric-method Man page
normalizeTagCount Man page
normalizeTagCount,CAGEset-method Man page
plotCorrelation Man page
plotCorrelation,CAGEset-method Man page
plotExpressionProfiles Man page
plotExpressionProfiles,CAGEset-method Man page
plotInterquantileWidth Man page
plotInterquantileWidth,CAGEset-method Man page
plotReverseCumulatives Man page
plotReverseCumulatives,CAGEset-method Man page
quantilePositions Man page
quantilePositions,CAGEset-method Man page
sampleLabels Man page
sampleLabels,CAGEset-method Man page
scoreShift Man page
scoreShift,CAGEset,character,character-method Man page
setColors Man page
setColors,CAGEset-method Man page
show,CAGEset-method Man page
show-methods Man page
tagClusters Man page
tagClusters,CAGEset-method Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.