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 (3.23)

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 "4.6") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BadRegionFinder")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Classification, Coverage, Sequencing, Software, WholeGenome
Version	1.39.0
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
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
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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	https://bioconductor.org/packages/BadRegionFinder/
Package Downloads Report	Download Stats