BRGenomics

DOI: 10.18129/B9.bioc.BRGenomics    

Tools for the Efficient Analysis of High-Resolution Genomics Data

Bioconductor version: Release (3.11)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.2
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package BRGenomics_1.0.2.tar.gz
Windows Binary BRGenomics_1.0.2.zip
macOS 10.13 (High Sierra) BRGenomics_1.0.2.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
Old Source Packages for BioC 3.11 Source Archive

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