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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 (3.19)

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BRGenomics")

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

Documentation

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

browseVignettes("BRGenomics")
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
NEWS Text

Details

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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Build Report Build Report

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/
Package Downloads Report Download Stats