| 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 |