BadRegionFinder

DOI: 10.18129/B9.bioc.BadRegionFinder    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BadRegionFinder.

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Bioconductor version: 3.8

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

Author: Sarah Sandmann

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BadRegionFinder")

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("BadRegionFinder")

 

PDF	R Script	Using BadRegionFinder
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Classification, Coverage, Sequencing, Software, WholeGenome
Version	1.10.0
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	LGPL-3
Depends
Imports	VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
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	BadRegionFinder_1.10.0.tar.gz
Windows Binary	BadRegionFinder_1.10.0.zip
Mac OS X 10.11 (El Capitan)	BadRegionFinder_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BadRegionFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BadRegionFinder
Package Short Url	http://bioconductor.org/packages/BadRegionFinder/
Package Downloads Report	Download Stats