Man pages for CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
| assignGeneID | Annotate ranges with gene ID. |
| assignMissingID | Annotate ranges with missing IDs. |
| assignTxID | Annotate ranges with transcript ID. |
| assignTxType | Annotate ranges with transcript type. |
| balanceBC | Balance statistic: Bhattacharyya coefficient (BC) |
| balanceD | Balance statistic: Andersson's D. |
| bwCommonGenome | Find a common genome for a series of BigWig files. |
| bwGenomeCompatibility | Check if BigWig-files are compatible with a given genome. |
| bwValid | Check if BigWig-files are valid. |
| calcBidirectionality | Calculate sample-wise bidirectionally of clusters. |
| calcComposition | Calculate composition of CAGE data. |
| calcPooled | Calculate pooled expression across all samples. |
| calcShape | Calculate Tag Cluster shapes |
| calcSupport | Calculate support of CAGE data. |
| calcTotalTags | Calculate the total number of CAGE tags across samples. |
| calcTPM | Calculate CAGE Tags-Per-Million (TPM) |
| checkCTSSs | Helper for checking files containing CTSSs |
| checkPeaked | Helper for checking cluster with peaks |
| checkPooled | Helper for checking pooled signal |
| clusterBidirectionally | Bidirectional clustering of pooled CTSSs. |
| clusterUnidirectionally | Unidirectional Clustering (Tag Clustering) of pooled CTSSs. |
| combineClusters | Combine two CAGE experiments. |
| convertBAM2BigWig | Extract CTSSs from BAM-files (EXPERIMENTAL) |
| convertBED2BigWig | Convert CTSSs stored in different file formats. |
| convertGRanges2GPos | Convert GRanges with scores to GPos |
| exampleDesign | Example CAGE Data |
| findLinks | Find nearby pairs of clusters and calculate pairwise... |
| findStretches | Find stretches of clusters |
| quantifyClusters | Quantify expression of clusters (TSSs or enhancers) by... |
| quantifyCTSSs | Quantify CAGE Transcriptions Start Sites (CTSSs) |
| quantifyCTSSs2 | Quantify CAGE Transcriptions Start Sites (CTSSs) |
| quantifyGenes | Quantify expression of genes |
| quickEnhancers | Identify and quantify enhancers. |
| quickGenes | Identify and quantify genes. |
| quickTSSs | Identify and quantify Transcription Start Sites (TSSs). |
| shapeEntropy | Shape statistic: Shannon Entropy |
| shapeIQR | Shape statitic: Interquartile range |
| shapeMean | Shape statistic: Mean |
| shapeMultimodality | Shape statistic: Multimodality |
| subsetByBidirectionality | Subset by sample-wise bidirectionality of clusters. |
| subsetByComposition | Subset by composition across samples |
| subsetBySupport | Subset by support across samples |
| swapRanges | Swap ranges in a GRanges. |
| swapScores | Swap scores in SummarizedExperiment |
| trackBalance | Create Genome Browser Track of bidirectional balance scores |
| trackClusters | Create genome browser track of clusters. |
| trackCTSS | Create Genome Browser track of CTSSs. |
| trackLinks | Create a genome browser track of links. |
| trimToPeak | Trim width of TCs by distance from TC peak |
| trimToPercentiles | Trim width of TCs to expression percentiles |
| tuneTagClustering | Determine the optimal pooled threshold for unidirectional tag... |
| utilsAggregateRows | Utility: Aggregate rows |
| utilsDeStrand | Utility: Split Genomic Ranges by strand |
| utilsScoreOverlaps | Utility: Counting overlaps taking into account scores |
| utilsSimplifyTxDb | Utility: Extract annotation hierachy from a TxDb. |
