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Bioconductor - BadRegionFinder

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

Bioconductor version: Release (3.21)

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")
Details biocViews Alignment, Classification, Coverage, Sequencing, Software, WholeGenome Version 1.36.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License LGPL-3 Depends Imports VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics System Requirements URL See More Package Archives

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

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