BRGenomics-package      BRGenomics: Tools for the Efficient Analysis of
                        High-Resolution Genomics Data
PROseq-data             PRO-seq data from Drosophila S2 cells
applyNFsGRanges         Apply normalization factors to GRanges object
binNdimensions          Generating and Aggregating Data Within
                        N-dimensional Bins
bootstrap-signal-by-position
                        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        Filtering and counting spike-in reads
getSpikeInNFs           Calculating spike-in normalization factors
getStrandedCoverage     Get strand-specific coverage
import-functions        Import basepair-resolution files
import_bam              Import bam files
intersectByGene         Intersect or reduce ranges according to gene
                        names
makeGRangesBRG          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.
