Man pages for charles-plessy/CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
| aggregateTagClusters | Aggregate TCs across all samples |
| annotateCTSS | Annotate and compute summary statistics |
| bam2CTSS | bam2CTSS |
| byCtss | Apply functions to identical CTSSes. |
| CAGEexp-class | CAGEr class to hold all data and metadata about one CAGE... |
| CAGEr-class | CAGEr objects |
| CAGEr_Multicore | Multicore support in CAGEr |
| CAGEr-package | CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression)... |
| coerceInBSgenome | coerceInBSgenome |
| consensusClusters | Get consensus clusters from CAGEr objects |
| ConsensusClusters-class | ConsensusClusters |
| consensusClustersDESeq2 | Export _consensus cluster_ expression data for DESeq2... |
| consensusClustersQuantile | Quantile metadata stored in CAGEr objects. |
| consensusClusters-set | Set consensus clusters from CAGEr objects |
| consensusClustersTpm | Extracting consensus clusters tpm matrix from CAGEr object |
| CTSS-class | CAGE Transcription Start Sites |
| CTSScoordinates | Genomic coordinates of TSSs from a 'CAGEr' object |
| CTSScumulativesTagClusters | Get/set CTSS cumulative TC or CC data |
| CTSSnormalizedTpm | Extracting normalized CAGE signal for TSSs from CAGEr objects |
| CTSStagCount | Raw CAGE TSSs expression counts |
| CTSStoGenes | Make a gene expression table. |
| cumulativeCTSSdistribution | Cumulative sums of CAGE counts along genomic regions |
| CustomConsensusClusters | Expression levels of consensus cluster |
| distclu | Distance clustering |
| dot-ctss_summary_for_clusters | Summarise CTSSs included in clusters |
| exampleCAGEexp | Example CAGEexp object. |
| exampleZv9_annot | Example zebrafish annotation data |
| exportToTrack | Converts TSSs and clusters of TSSs to a genome browser track... |
| expressionClasses | Extract labels of _expression classes_ |
| FANTOM5humanSamples | FANTOM5 human samples |
| FANTOM5mouseSamples | FANTOM5 mouse samples |
| filteredCTSSidx | The 'filteredCTSSidx()' function is in _CAGEr_ functions to... |
| flagByUpstreamSequences | Filter by upstream sequences |
| flagLowExpCTSS | Flag CTSSes based on sample expression |
| GeneExpDESeq2 | Export gene expression data for DESeq2 analysis |
| GeneExpSE | Retreives the SummarizedExperiment containing gene expression... |
| genomeName | Extracting genome name from CAGEr objects |
| getCTSS | Reading CAGE data from input file(s) and detecting TSSs |
| getExpressionProfiles | CAGE data based expression clustering |
| getShiftingPromoters | Select consensus clusters with shifting score above threshold |
| hanabi | Calcultate richness in preparation for plotting |
| hanabi-class | Hanabi class |
| hanabiPlot | hanabiPlot |
| import.bam | import.bam |
| import.bam.ctss | import.bam.ctss |
| import.bedCTSS | import.bedCTSS |
| import.bedmolecule | import.bedmolecule |
| import.bedScore | import.bedScore |
| import.CAGEscanMolecule | import.CAGEscanMolecule |
| import.CTSS | import.CTSS |
| importPublicData | importPublicData |
| inputFiles | Extracting paths to input files from CAGEr objects |
| inputFilesType | Input file formats for CAGEr objects |
| librarySizes | Extracting library sizes from CAGEr objects |
| loadFileIntoGPos | loadFileIntoGPos |
| mapStats | Process mapping statistics |
| mapStatsScopes | mapStats scopes |
| mergeCAGEsets | Merge two CAGEr objects into one |
| mergeSamples | Merge CAGE samples |
| moleculesGR2CTSS | moleculesGR2CTSS |
| normalizeTagCount | Normalizing raw CAGE tag count |
| paraclu | Parametric clustering |
| parseCAGEscanBlocksToGrangeTSS | parseCAGEscanBlocksToGrangeTSS |
| plotAnnot | Plot annotation statistics |
| plotCorrelation | Pairwise scatter plots and correlations of CAGE signal |
| plotExpressionProfiles | Plot CAGE expression profiles |
| plot.hanabi | Plotting Hanabi objects |
| plotInterquantileWidth | Plot cluster widths |
| plotReverseCumulatives | Plot reverse cumulative number of CAGE tags per CTSS |
| powerLaw | .powerLaw |
| quantilePositions | Determine CTSS quantile positions within clusters |
| QuantileWidthFunctions | Get quantile positions |
| quickEnhancers | Identify and quantify enhancers. |
| ranges2annot | Hierarchical annotation of genomic regions. |
| ranges2genes | ranges2genes |
| ranges2names | ranges2names |
| resetCAGEexp | Reset a CAGEexp object |
| rowsum.RleDataFrame | rowsum function for Rle DataFrames |
| rowSums.RleDataFrame | rowSums function for Rle DataFrames |
| sampleLabels | Get and set sample labels |
| scoreShift | Calculate promoter shifting score |
| seqNameTotalsSE | Retreives the SummarizedExperiment containing chromosome... |
| setColors | Set colors for samples |
| strandInvaders | Detect and remove strand invasion artefacts |
| summariseChrExpr | Expression levels by chromosomes |
| tagClusters | Extract tag clusters (TCs) for individual CAGE experiments |
| TagClusters-class | TagClusters |
| TSSlogo | TSS logo |
