BRGenomics

DOI: 10.18129/B9.bioc.BRGenomics    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BRGenomics.

Tools for the Efficient Analysis of High-Resolution Genomics Data

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	ATACSeq, ChIPSeq, Coverage, DataImport, GeneExpression, GeneRegulation, Normalization, RNASeq, Sequencing, Software, Transcription
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors
Imports	GenomicRanges, parallel, IRanges, stats, Rsamtools, GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings
SystemRequirements
Enhances
URL	https://mdeber.github.io
BugReports	https://github.com/mdeber/BRGenomics/issues
Depends On Me
Imports Me	EpiCompare
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BRGenomics_1.8.0.tar.gz
Windows Binary	BRGenomics_1.8.0.zip
macOS Binary (x86_64)	BRGenomics_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BRGenomics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BRGenomics
Package Short Url	https://bioconductor.org/packages/BRGenomics/
Package Downloads Report	Download Stats