DOI: 10.18129/B9.bioc.BRGenomics  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BRGenomics.

Tools for the Efficient Analysis of High-Resolution Genomics Data

Bioconductor version: 3.16

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")):


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HTML R Script 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 Overview
HTML R Script Profile Plots and Bootstrapping
HTML R Script Sequence Extraction
HTML R Script Signal Counting
HTML R Script Spike-in Normalization
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, ChIPSeq, Coverage, DataImport, GeneExpression, GeneRegulation, Normalization, RNASeq, Sequencing, Software, Transcription
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License Artistic-2.0
Depends R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors
Imports GenomicRanges, parallel, IRanges, stats, Rsamtools, GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods
Suggests BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings
Depends On Me
Imports Me EpiCompare
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