BadRegionFinder

This is the released version of BadRegionFinder; for the devel version, see BadRegionFinder.

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

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DOI: 10.18129/B9.bioc.BadRegionFinder

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Classification, Coverage, Sequencing, Software, WholeGenome

Version 1.38.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 years)

License LGPL-3

Depends

Imports VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics

System Requirements

URL

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_1.38.0.tar.gz

Windows Binary (x86_64) BadRegionFinder_1.37.0.zip (64-bit only)

macOS Binary (x86_64) BadRegionFinder_1.38.0.tgz

macOS Binary (arm64) BadRegionFinder_1.38.0.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/

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