# Tools for the Efficient Analysis of High-Resolution Genomics Data

## Documentation for package ‘BRGenomics’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

BRGenomics-package | BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data
aggregateByNdimBins | Generating and Aggregating Data Within N-dimensional Bins
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
BRGenomics | BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data
densityInNdimBins | Generating and Aggregating Data Within N-dimensional Bins
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
getSpikeInReads | Filtering and counting spike-in reads
getStrandedCoverage | Get strand-specific coverage
import-functions | Import basepair-resolution files
import_bam | Import bam files
import_bam_ATACseq | Import bam files
import_bam_PROcap | Import bam files
import_bam_PROseq | Import bam files
import_bedGraph | Import basepair-resolution files
import_bigWig | Import basepair-resolution files
intersectByGene | Intersect or reduce ranges according to gene names
isBRG | Constructing and checking for base-pair resolution GRanges objects
makeGRangesBRG | Constructing and checking for base-pair resolution GRanges objects
mergeGRangesData | Merge GRanges objects
mergeReplicates | Merge replicates of basepair-resolution GRanges objects
metaSubsample | Bootstrapping Mean Signal by Position for Metaplotting
metaSubsampleMatrix | Bootstrapping Mean Signal by Position for Metaplotting
PROseq | PRO-seq data from Drosophila S2 cells
PROseq-data | PRO-seq data from Drosophila S2 cells
PROseq_paired | PRO-seq data from Drosophila S2 cells
reduceByGene | Intersect or reduce ranges according to gene names
removeSpikeInReads | Filtering and counting spike-in reads
spikeInNormGRanges | Calculating spike-in normalization factors
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.