Function reference • BRGenomics

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`BRGenomics-package` `BRGenomics`	BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data
`PROseq` `PROseq_paired`	PRO-seq data from Drosophila S2 cells
`applyNFsGRanges()`	Apply normalization factors to GRanges object
`binNdimensions()` `aggregateByNdimBins()` `densityInNdimBins()`	Generating and Aggregating Data Within N-dimensional Bins
`metaSubsample()` `metaSubsampleMatrix()`	Bootstrapping Mean Signal by Position for Metaplotting
`genebodies()`	Extract Genebodies
`getCountsByPositions()`	Get signal counts at each position within regions of interest
`getCountsByRegions()`	Get signal counts in regions of interest
`getDESeqDataSet()`	Get DESeqDataSet objects for downstream analysis
`getDESeqResults()`	Get DESeq2 results using reduced dispersion matrices
`getMaxPositionsBySignal()`	Find sites with max signal in regions of interest
`getPausingIndices()`	Calculate pausing indices from user-supplied promoters & genebodies
`getSpikeInCounts()` `removeSpikeInReads()` `getSpikeInReads()`	Filtering and counting spike-in reads
`getSpikeInNFs()` `spikeInNormGRanges()`	Calculating spike-in normalization factors
`getStrandedCoverage()`	Get strand-specific coverage
`import_bigWig()` `import_bedGraph()`	Import basepair-resolution files
`import_bam()` `import_bam_PROseq()` `import_bam_PROcap()` `import_bam_ATACseq()`	Import bam files
`intersectByGene()` `reduceByGene()`	Intersect or reduce ranges according to gene names
`makeGRangesBRG()` `isBRG()`	Constructing and checking for base-pair resolution GRanges objects
`mergeGRangesData()`	Merge GRanges objects
`mergeReplicates()`	Merge replicates of basepair-resolution GRanges objects
`subsampleBySpikeIn()`	Randomly subsample reads according to spike-in normalization
`subsampleGRanges()`	Randomly subsample reads from GRanges dataset
`subsetRegionsBySignal()`	Subset regions of interest by quantiles of overlapping signal
`tidyChromosomes()`	Remove odd chromosomes from GRanges objects
`txs_dm6_chr4`	Ensembl transcripts for Drosophila melanogaster, dm6, chromosome 4.

Reference

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