assignGeneID | Annotate ranges with gene ID. |
assignGeneID-method | Annotate ranges with gene ID. |
assignMissingID | Annotate ranges with missing IDs. |
assignMissingID-method | Annotate ranges with missing IDs. |
assignTxID | Annotate ranges with transcript ID. |
assignTxID-method | Annotate ranges with transcript ID. |
assignTxType | Annotate ranges with transcript type. |
assignTxType-method | 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. |
bwValid-method | Check if BigWig-files are valid. |
calcBidirectionality | Calculate sample-wise bidirectionally of clusters. |
calcBidirectionality-method | Calculate sample-wise bidirectionally of clusters. |
calcComposition | Calculate composition of CAGE data. |
calcPooled | Calculate pooled expression across all samples. |
calcShape | Calculate Tag Cluster shapes |
calcShape-method | 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) |
checkPeaked | Helper for checking cluster with peaks |
checkPooled | Helper for checking pooled signal |
clusterBidirectionally | Bidirectional clustering of pooled CTSSs. |
clusterBidirectionally-method | Bidirectional clustering of pooled CTSSs. |
clusterUnidirectionally | Unidirectional Clustering (Tag Clustering) of pooled CTSSs. |
clusterUnidirectionally-method | Unidirectional Clustering (Tag Clustering) of pooled CTSSs. |
combineClusters | Combine two CAGE experiments. |
combineClusters-method | Combine two CAGE experiments. |
exampleBidirectional | Example CAGE Data |
exampleCTSSs | Example CAGE Data |
exampleDesign | Example CAGE Data |
exampleGenes | Example CAGE Data |
exampleUnidirectional | Example CAGE Data |
findLinks | Find nearby pairs of clusters and calculate pairwise correlations. |
findLinks-method | Find nearby pairs of clusters and calculate pairwise correlations. |
findStretches | Find stretches of clusters |
findStretches-method | Find stretches of clusters |
quantifyClusters | Quantify expression of clusters (TSSs or enhancers) by summing CTSSs within clusters. |
quantifyCTSSs | Quantify CAGE Transcriptions Start Sites (CTSSs) |
quantifyGenes | Quantify expression of genes |
quickEnhancers | Identify and quantify enhancers. |
quickTSSs | Identify and quantify Transcription Start Sites (TSSs). |
shapeEntropy | Shape statistic: Shannon Entropy |
shapeIQR | Shape statitic: Interquartile range |
shapeMultimodality | Shape statistic: Multimodality |
subsetByBidirectionality | Subset by sample-wise bidirectionality of clusters. |
subsetByBidirectionality-method | 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. |
swapRanges-method | Swap ranges in a GRanges. |
swapScores | Swap scores in SummarizedExperiment |
trackBalance | Create Genome Browser Track of bidirectional balance scores |
trackBalance-method | Create Genome Browser Track of bidirectional balance scores |
trackClusters | Create genome browser track of clusters. |
trackClusters-method | Create genome browser track of clusters. |
trackCTSS | Create Genome Browser track of CTSSs. |
trackCTSS-method | Create Genome Browser track of CTSSs. |
trackLinks | Create a genome browser track of links. |
trimToPeak | Trim width of TCs by distance from TC peak |
trimToPeak-method | Trim width of TCs by distance from TC peak |
trimToPercentiles | Trim width of TCs to expression percentiles |
trimToPercentiles-method | Trim width of TCs to expression percentiles |
tuneTagClustering | Determine the optimal pooled threshold for unidirectional tag clustering. |
tuneTagClustering-method | Determine the optimal pooled threshold for unidirectional tag clustering. |