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

## Documentation for package ‘CAGEr’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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