BRGenomics

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BRGenomics.

Tools for the Efficient Analysis of High-Resolution Genomics Data


Bioconductor version: 3.17

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 "4.3") and enter:


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

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 1.12.0
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
Enhances
Depends On Me
Imports Me EpiCompare
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package BRGenomics_1.12.0.tar.gz
Windows Binary BRGenomics_1.12.0.zip
macOS Binary (x86_64) BRGenomics_1.12.0.tgz
macOS Binary (arm64) BRGenomics_1.12.0.tgz
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
Old Source Packages for BioC 3.17 Source Archive