CNVPanelizer: Reliable CNV detection in targeted sequencing applications

A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.

AuthorCristiano Oliveira [aut], Thomas Wolf [aut, cre], Albrecht Stenzinger [ctb], Volker Endris [ctb], Nicole Pfarr [ctb], Benedikt Brors [ths], Wilko Weichert [ths]
Date of publicationNone
MaintainerThomas Wolf <thomas_wolf71@gmx.de>
LicenseGPL-3
Version1.4.0

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Files in this package

CNVPanelizer/DESCRIPTION
CNVPanelizer/NAMESPACE
CNVPanelizer/NEWS
CNVPanelizer/R
CNVPanelizer/R/FolderAnalysis_functions.R CNVPanelizer/R/SyntheticData.R
CNVPanelizer/README.md
CNVPanelizer/build
CNVPanelizer/build/vignette.rds
CNVPanelizer/data
CNVPanelizer/data/referenceReadCounts.RData
CNVPanelizer/data/sampleReadCounts.RData
CNVPanelizer/inst
CNVPanelizer/inst/doc
CNVPanelizer/inst/doc/CNVPanelizer.R
CNVPanelizer/inst/doc/CNVPanelizer.Rnw
CNVPanelizer/inst/doc/CNVPanelizer.pdf
CNVPanelizer/inst/extdata
CNVPanelizer/inst/extdata/regions.bed
CNVPanelizer/inst/unitTests
CNVPanelizer/inst/unitTests/test_testing.R
CNVPanelizer/man
CNVPanelizer/man/Background.Rd CNVPanelizer/man/BedToGenomicRanges.Rd CNVPanelizer/man/BootList.Rd CNVPanelizer/man/CNVPanelizer-package.Rd CNVPanelizer/man/CombinedNormalizedCounts.Rd CNVPanelizer/man/IndexMultipleBams.Rd CNVPanelizer/man/PlotBootstrapDistributions.Rd CNVPanelizer/man/ReadCountsFromBam.Rd CNVPanelizer/man/ReadXLSXToList.Rd CNVPanelizer/man/ReportTables.Rd CNVPanelizer/man/WriteListToXLSX.Rd CNVPanelizer/man/referenceReadCounts.Rd CNVPanelizer/man/sampleReadCounts.Rd
CNVPanelizer/run_tests.R
CNVPanelizer/tests
CNVPanelizer/tests/runTests.R
CNVPanelizer/vignettes
CNVPanelizer/vignettes/CNVPanelizer.Rnw
CNVPanelizer/vignettes/CNVPanelizer.bib

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