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CAGEr (version 1.14.0)

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

Description

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

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Version

Version

1.14.0

License

GPL-3

Maintainer

Vanja Haberle

Last Published

February 15th, 2017

Functions in CAGEr (1.14.0)

exportToBed

Creating BED tracks of TSSs and clusters of TSSs
getExpressionProfiles

CAGE data based expression clustering
tagClusters

Extracting tag clusters (TCs) for individual CAGE experiment from CAGEset object
consensusClusters

Extracting consensus clusters from CAGEset object
aggregateTagClusters

Aggregating tag clusters across multiple CAGE datasets
getShiftingPromoters

Selecting consensus clusters with shifting score above specified threshold
exampleCAGEset

Example CAGEset object with zebrafish CAGE data
extractExpressionClass

Extracting elements of the specified expression class
exportCTSStoBedGraph

Creating bedGraph/bigWig tracks of CAGE transcription starts sites
importPublicData

Importing publicly available CAGE data from various resources
show-methods

Methods for function show
scoreShift

Calculating promoter shifting score
inputFilesType

Extracting type of input files from CAGEset object
setColors

Setting colors for samples
sampleLabels

Extracting CAGE datasets labels from CAGEset object
cumulativeCTSSdistribution

Calculating cumulative sum of CAGE signal along genomic region
quantilePositions

Determining positions of CAGE signal quantiles within genomic region
clusterCTSS

Clustering CTSSs into tag clusters (TCs)
consensusClustersTpm

Extracting consensus clusters tpm matrix from CAGEset object
getCTSS

Reading CAGE data from input file(s) and detecting TSSs
expressionClasses

Extracting labels of expression classes
inputFiles

Extracting paths to input files from CAGEset object
mergeSamples

Merging CAGE datasets (samples)
CAGEset-class

Class "CAGEset"
CTSSclusteringMethod

Extracting CTSS clustering method from CAGEset object
plotExpressionProfiles

Plotting expression profiles derived from CAGE data
plotReverseCumulatives

Plotting reverse cumulative number of CAGE tags per CTSS
plotCorrelation

Plotting pairwise scatter plots of CAGE signal and calculating correlation between samples
CTSSnormalizedTpm

Extracting normalized CAGE signal for TSSs from CAGEset object
FANTOM5humanSamples

List of FANTOM5 human CAGE samples
CTSScoordinates

Extracting genomic coordinates of TSSs from CAGEset object
CAGEr-package

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

Extracting CAGE tag count for TSSs from CAGEset object
FANTOM5mouseSamples

List of FANTOM5 mouse CAGE samples
normalizeTagCount

Normalizing raw CAGE tag count
mergeCAGEsets

Merging two CAGEset objects into one
genomeName

Extracting genome name from CAGEset object
librarySizes

Extracting library sizes from CAGEset object
plotInterquantileWidth

Plotting distribution of interquantile width