# Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

## Documentation for package ‘CAGEfightR’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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)
checkCTSSs | Helper for checking files containing CTSSs
checkCTSSs-method | 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.
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.
convertBAM2BigWig | Extract CTSSs from BAM-files (EXPERIMENTAL)
convertBED2BedGraph | Convert CTSSs stored in different file formats.
convertBED2BigWig | Convert CTSSs stored in different file formats.
convertBedGraph2BED | Convert CTSSs stored in different file formats.
convertBedGraph2BigWig | Convert CTSSs stored in different file formats.
convertBigWig2BED | Convert CTSSs stored in different file formats.
convertBigWig2BedGraph | Convert CTSSs stored in different file formats.
convertGRanges2GPos | Convert GRanges with scores to GPos
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)
quantifyCTSSs-method | 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.
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.
utilsAggregateRows | Utility: Aggregate rows
utilsAggregateRows-method | 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.