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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BBCAnalyzer")
AuthorSarah Sandmann
Bioconductor views Alignment Coverage GeneticVariability SNP Sequencing
Date of publicationNone
MaintainerSarah Sandmann <sarah.sandmann@uni-muenster.de>
LicenseLGPL-3
Version1.6.0

View on Bioconductor

Files

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

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

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

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