BBCAnalyzer

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BBCAnalyzer.

BBCAnalyzer: an R/Bioconductor package for visualizing base counts


Bioconductor version: 3.10

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

Author: Sarah Sandmann

Maintainer: Sarah Sandmann <sarah.sandmann at uni-muenster.de>

Citation (from within R, enter citation("BBCAnalyzer")):

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("BBCAnalyzer")

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("BBCAnalyzer")
Using BBCAnalyzer PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Coverage, GeneticVariability, SNP, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License LGPL-3
Depends
Imports SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings
System Requirements
URL
See More
Suggests BSgenome.Hsapiens.UCSC.hg19
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 BBCAnalyzer_1.16.0.tar.gz
Windows Binary BBCAnalyzer_1.16.0.zip
Mac OS X 10.11 (El Capitan) BBCAnalyzer_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BBCAnalyzer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BBCAnalyzer
Bioc Package Browser https://code.bioconductor.org/browse/BBCAnalyzer/
Package Short Url https://bioconductor.org/packages/BBCAnalyzer/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive