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Tools for the Efficient Analysis of High-Resolution Genomics Data

Bioconductor version: Release (3.18)

This package provides useful and efficient utilites for the analysis of high-resolution genomic data using standard Bioconductor methods and classes. BRGenomics is feature-rich and simplifies a number of post-alignment processing steps and data handling. Emphasis is on efficient analysis of multiple datasets, with support for normalization and blacklisting. Included are functions for: spike-in normalizing data; generating basepair-resolution readcounts and coverage data (e.g. for heatmaps); importing and processing bam files (e.g. for conversion to bigWig files); generating metaplots/metaprofiles (bootstrapped mean profiles) with confidence intervals; conveniently calling DESeq2 without using sample-blind estimates of genewise dispersion; among other features.

Author: Mike DeBerardine [aut, cre]

Maintainer: Mike DeBerardine <mike.deberardine at>

Citation (from within R, enter citation("BRGenomics")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analyzing Multiple Datasets HTML R Script
DESeq2 with Global Perturbations HTML R Script
Getting Started HTML R Script
Importing and Modifying Annotations HTML R Script
Importing and Processing Data HTML R Script
Overview HTML
Profile Plots and Bootstrapping HTML R Script
Sequence Extraction HTML R Script
Signal Counting HTML R Script
Spike-in Normalization HTML R Script
Reference Manual PDF


biocViews ATACSeq, ChIPSeq, Coverage, DataImport, GeneExpression, GeneRegulation, Normalization, RNASeq, Sequencing, Software, Transcription
Version 1.14.1
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License Artistic-2.0
Depends R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors
Imports GenomicRanges, parallel, IRanges, stats, Rsamtools, GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods
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Suggests BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BRGenomics_1.14.1.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) BRGenomics_1.14.1.tgz
macOS Binary (arm64) BRGenomics_1.14.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
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Old Source Packages for BioC 3.18 Source Archive