BadRegionFinder

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


Bioconductor version: Release (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
Using BadRegionFinder PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Classification, Coverage, Sequencing, Software, WholeGenome
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8.5 years)
License LGPL-3
Depends
Imports VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics
System Requirements
URL
See More
Suggests BSgenome.Hsapiens.UCSC.hg19
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package BadRegionFinder_1.32.0.tar.gz
Windows Binary BadRegionFinder_1.32.0.zip
macOS Binary (x86_64) BadRegionFinder_1.32.0.tgz
macOS Binary (arm64) BadRegionFinder_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BadRegionFinder
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BadRegionFinder
Bioc Package Browser https://code.bioconductor.org/browse/BadRegionFinder/
Package Short Url https://bioconductor.org/packages/BadRegionFinder/
Package Downloads Report Download Stats