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BadRegionFinder

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


Bioconductor version: Release (3.18)

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 "4.3") 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 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
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 BadRegionFinder_1.30.0.tar.gz
Windows Binary BadRegionFinder_1.30.0.zip
macOS Binary (x86_64) BadRegionFinder_1.30.0.tgz
macOS Binary (arm64) BadRegionFinder_1.30.0.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