BRGenomics
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BRGenomics.
Tools for the Efficient Analysis of High-Resolution Genomics Data
Bioconductor version: 3.12
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 gmail.com>
citation("BRGenomics")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, ChIPSeq, Coverage, DataImport, GeneExpression, GeneRegulation, Normalization, RNASeq, Sequencing, Software, Transcription |
| Version | 1.2.0 |
| 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 | |
| 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_1.2.0.tar.gz |
| Windows Binary | BRGenomics_1.2.0.zip |
| macOS 10.13 (High Sierra) | BRGenomics_1.2.0.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 3.12 | Source Archive |