Man pages for ge11232002/CAGEr
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 |
| 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... |
