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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BadRegionFinder")
AuthorSarah Sandmann
Bioconductor views Alignment Classification Coverage Sequencing WholeGenome
Date of publicationNone
MaintainerSarah Sandmann <sarah.sandmann@uni-muenster.de>
LicenseLGPL-3
Version1.4.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BadRegionFinder.R R/additional.R R/plots.R R/reports.R
build
build/partial.rdb
build/vignette.rds
inst
inst/doc
inst/doc/BadRegionFinder.R
inst/doc/BadRegionFinder.Rnw
inst/doc/BadRegionFinder.pdf
inst/extdata
inst/extdata/SampleNames.txt
inst/extdata/SampleNames2.txt
inst/extdata/Test2_454.bai
inst/extdata/Test2_454.bam
inst/extdata/Test2_ion.bai
inst/extdata/Test2_ion.bam
inst/extdata/Test_454.bai
inst/extdata/Test_454.bam
inst/extdata/Test_ion.bai
inst/extdata/Test_ion.bam
inst/extdata/regionsOfInterest.bed
inst/extdata/targetRegions.bed
inst/extdata/targetRegions2.bed
man
man/BadRegionFinder-package.Rd man/determineCoverage.Rd man/determineCoverageQuality.Rd man/determineQuantiles.Rd man/determineRegionsOfInterest.Rd man/plotDetailed.Rd man/plotSummary.Rd man/plotSummaryGenes.Rd man/reportBadRegionsDetailed.Rd man/reportBadRegionsGenes.Rd man/reportBadRegionsSummary.Rd
vignettes
vignettes/BadRegionFinder.Rnw
vignettes/bibpaper.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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