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


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Documentation for package ‘CAGEfightR’ version 1.0.0

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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.
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)
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
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.
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.