BRGenomics
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.20 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see BRGenomics.
Tools for the Efficient Analysis of High-Resolution Genomics Data
Bioconductor version: Release (3.20)
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("BRGenomics")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual |
Details
| biocViews | ATACSeq, ChIPSeq, Coverage, DataImport, GeneExpression, GeneRegulation, Normalization, RNASeq, Sequencing, Software, Transcription |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/BRGenomics |
| Source Repository (Developer Access) | git clone [email protected]:packages/BRGenomics |
| Package Short Url | https://bioconductor.org/packages/BRGenomics/ |
| Package Downloads Report | Download Stats |