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) |
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 tracks of CAGE transcription starts sites |
exportCTSStoBedGraph-method | Creating bedGraph 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 |
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 |