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.
|Date of publication||None|
|Maintainer||Sarah Sandmann <firstname.lastname@example.org>|
BadRegionFinder-package: BadRegionFinder: an R/Bioconductor package for identifying...
determineCoverage: Determines the coverage (recommended for whole-genome...
determineCoverageQuality: Classifies the determined coverage
determineQuantiles: Determines basewise user-defined quantiles
determineRegionsOfInterest: Determines the regions of interest
plotDetailed: Plots a more detailed overview of the coverage quality
plotSummary: Plots a summary of the coverage quality
plotSummaryGenes: Plots a summary of the coverage quality concerning the genes...
reportBadRegionsDetailed: Gives a detailed report on the coverage quality
reportBadRegionsGenes: Sums up the coverage quality on a gene basis
reportBadRegionsSummary: Sums up the coverage quality