DOI: 10.18129/B9.bioc.BadRegionFinder    

This is the development version of BadRegionFinder; for the stable release version, see BadRegionFinder.

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

Bioconductor version: Development (3.9)

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>

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


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

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("BadRegionFinder", version = "3.9")

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script Using BadRegionFinder
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Classification, Coverage, Sequencing, Software, WholeGenome
Version 1.11.0
In Bioconductor since BioC 3.3 (R-3.3) (3 years)
License LGPL-3
Imports VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics
Suggests BSgenome.Hsapiens.UCSC.hg19
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_1.11.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) BadRegionFinder_1.11.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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