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

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Documentation for package ‘CAGEfightR’ version 1.22.0

• 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.