BBCAnalyzer: BBCAnalyzer: an R/Bioconductor package for visualizing base counts

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BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

Author
Sarah Sandmann
Date of publication
None
Maintainer
Sarah Sandmann <sarah.sandmann@uni-muenster.de>
License
LGPL-3
Version
1.4.0

View on Bioconductor

Man pages

analyzeBases
Analyze the bases at all previously defined positions
analyzeBasesPlotOnly
Plots the number of reads at all previously defined positions
BBCAnalyzer-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("BBCAnalyzer")}

Files in this package

BBCAnalyzer/DESCRIPTION
BBCAnalyzer/NAMESPACE
BBCAnalyzer/NEWS
BBCAnalyzer/R
BBCAnalyzer/R/BBCAnalyzer.R
BBCAnalyzer/R/determineTarget_analyzeReads.R
BBCAnalyzer/R/frequency.R
BBCAnalyzer/R/plot.R
BBCAnalyzer/R/report.R
BBCAnalyzer/build
BBCAnalyzer/build/partial.rdb
BBCAnalyzer/build/vignette.rds
BBCAnalyzer/inst
BBCAnalyzer/inst/doc
BBCAnalyzer/inst/doc/BBCAnalyzer.R
BBCAnalyzer/inst/doc/BBCAnalyzer.Rnw
BBCAnalyzer/inst/doc/BBCAnalyzer.pdf
BBCAnalyzer/inst/extdata
BBCAnalyzer/inst/extdata/Example_454.bai
BBCAnalyzer/inst/extdata/Example_454.bam
BBCAnalyzer/inst/extdata/Example_454.vcf
BBCAnalyzer/inst/extdata/Example_IonTorrent.bai
BBCAnalyzer/inst/extdata/Example_IonTorrent.bam
BBCAnalyzer/inst/extdata/Example_IonTorrent.vcf
BBCAnalyzer/inst/extdata/Example_IonTorrent_small.bai
BBCAnalyzer/inst/extdata/Example_IonTorrent_small.bam
BBCAnalyzer/inst/extdata/SampleNames.txt
BBCAnalyzer/inst/extdata/SampleNames_small.txt
BBCAnalyzer/inst/extdata/dbsnp_138.part.vcf.gz
BBCAnalyzer/inst/extdata/dbsnp_138.part.vcf.gz.tbi
BBCAnalyzer/inst/extdata/targetRegions.txt
BBCAnalyzer/inst/extdata/targetRegions2.txt
BBCAnalyzer/inst/extdata/targetRegions_small.txt
BBCAnalyzer/man
BBCAnalyzer/man/BBCAnalyzer-package.Rd
BBCAnalyzer/man/analyzeBases.Rd
BBCAnalyzer/man/analyzeBasesPlotOnly.Rd
BBCAnalyzer/vignettes
BBCAnalyzer/vignettes/BBCAnalyzer.Rnw
BBCAnalyzer/vignettes/Example_454.png
BBCAnalyzer/vignettes/Example_IonTorrent.png
BBCAnalyzer/vignettes/Example_IonTorrent_small.png
BBCAnalyzer/vignettes/bibpaper.bib
BBCAnalyzer/vignettes/chr20;31024054.png
BBCAnalyzer/vignettes/chr21;36206893.png
BBCAnalyzer/vignettes/chr21;44514970.png
BBCAnalyzer/vignettes/chr21;44514970_1.png
BBCAnalyzer/vignettes/chr2;25469913.png
BBCAnalyzer/vignettes/chr4;106157698.png
BBCAnalyzer/vignettes/chr7;148543694.png
BBCAnalyzer/vignettes/chr7;148543695.png