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This is the development version of BRGenomics; for the stable release version, see BRGenomics.

Tools for the Efficient Analysis of High-Resolution Genomics Data

Bioconductor version: Development (3.19)

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 gmail.com>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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 1.15.0
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
System Requirements
URL https://mdeber.github.io
Bug Reports https://github.com/mdeber/BRGenomics/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings
Linking To
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Package Archives

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

Source Package BRGenomics_1.15.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/BRGenomics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BRGenomics
Bioc Package Browser https://code.bioconductor.org/browse/BRGenomics/
Package Short Url https://bioconductor.org/packages/BRGenomics/
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