Man pages for CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

assignGeneIDAnnotate ranges with gene ID.
assignMissingIDAnnotate ranges with missing IDs.
assignTxIDAnnotate ranges with transcript ID.
assignTxTypeAnnotate ranges with transcript type.
balanceBCBalance statistic: Bhattacharyya coefficient (BC)
balanceDBalance statistic: Andersson's D.
bwCommonGenomeFind a common genome for a series of BigWig files.
bwGenomeCompatibilityCheck if BigWig-files are compatible with a given genome.
bwValidCheck if BigWig-files are valid.
calcBidirectionalityCalculate sample-wise bidirectionally of clusters.
calcCompositionCalculate composition of CAGE data.
calcPooledCalculate pooled expression across all samples.
calcShapeCalculate Tag Cluster shapes
calcSupportCalculate support of CAGE data.
calcTotalTagsCalculate the total number of CAGE tags across samples.
calcTPMCalculate CAGE Tags-Per-Million (TPM)
checkCTSSsHelper for checking files containing CTSSs
checkPeakedHelper for checking cluster with peaks
checkPooledHelper for checking pooled signal
clusterBidirectionallyBidirectional clustering of pooled CTSSs.
clusterUnidirectionallyUnidirectional Clustering (Tag Clustering) of pooled CTSSs.
combineClustersCombine two CAGE experiments.
convertBAM2BigWigExtract CTSSs from BAM-files (EXPERIMENTAL)
convertBED2BigWigConvert CTSSs stored in different file formats.
convertGRanges2GPosConvert GRanges with scores to GPos
exampleDesignExample CAGE Data
findLinksFind nearby pairs of clusters and calculate pairwise...
findStretchesFind stretches of clusters
quantifyClustersQuantify expression of clusters (TSSs or enhancers) by...
quantifyCTSSsQuantify CAGE Transcriptions Start Sites (CTSSs)
quantifyCTSSs2Quantify CAGE Transcriptions Start Sites (CTSSs)
quantifyGenesQuantify expression of genes
quickEnhancersIdentify and quantify enhancers.
quickGenesIdentify and quantify genes.
quickTSSsIdentify and quantify Transcription Start Sites (TSSs).
shapeEntropyShape statistic: Shannon Entropy
shapeIQRShape statitic: Interquartile range
shapeMeanShape statistic: Mean
shapeMultimodalityShape statistic: Multimodality
subsetByBidirectionalitySubset by sample-wise bidirectionality of clusters.
subsetByCompositionSubset by composition across samples
subsetBySupportSubset by support across samples
swapRangesSwap ranges in a GRanges.
swapScoresSwap scores in SummarizedExperiment
trackBalanceCreate Genome Browser Track of bidirectional balance scores
trackClustersCreate genome browser track of clusters.
trackCTSSCreate Genome Browser track of CTSSs.
trackLinksCreate a genome browser track of links.
trimToPeakTrim width of TCs by distance from TC peak
trimToPercentilesTrim width of TCs to expression percentiles
tuneTagClusteringDetermine the optimal pooled threshold for unidirectional tag...
utilsAggregateRowsUtility: Aggregate rows
utilsDeStrandUtility: Split Genomic Ranges by strand
utilsScoreOverlapsUtility: Counting overlaps taking into account scores
utilsSimplifyTxDbUtility: Extract annotation hierachy from a TxDb.
CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.