DOI: 10.18129/B9.bioc.BRGenomics    

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 (3.12)

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 1.1.3
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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
Suggests Me
Links To Me
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