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.

AuthorSarah Sandmann
Date of publicationNone
MaintainerSarah Sandmann <sarah.sandmann@uni-muenster.de>
LicenseLGPL-3
Version1.2.0

View on Bioconductor

Files in this package

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

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

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