Package: CNVPanelizer 1.37.0
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.
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CNVPanelizer_1.37.0.tar.gz
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CNVPanelizer.pdf |CNVPanelizer.html✨
CNVPanelizer/json (API)
NEWS
# Install 'CNVPanelizer' in R: |
install.packages('CNVPanelizer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- referenceReadCounts - Reference sample data
- sampleReadCounts - Test sample data
On BioConductor:CNVPanelizer-1.37.0(bioc 3.20)CNVPanelizer-1.36.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:d0277729f7
Exports:BackgroundBedToGenomicRangesBootListCNVPanelizerCNVPanelizerFromReadCountsCNVPanelizerFromReadCountsHELPERCollectColumnFromAllReportTablesCombinedNormalizedCountsIndexMultipleBamsNormalizeCountsPlotBootstrapDistributionsReadCountsFromBamReadXLSXToListReportTablesRunCNVPanelizerShinySelectReferenceSetByInterquartileRangeSelectReferenceSetByKmeansSelectReferenceSetByPercentilSelectReferenceSetFromReadCountsStatusHeatmapWriteListToXLSX
Dependencies:askpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbriobslibcachemcallrcaToolsclicodetoolscolorspacecommonmarkcpp11crayoncurldescdiffobjdigestevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshtmltoolshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothlabelinglambda.rlaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeNOISeqopensslopenxlsxpillarpkgbuildpkgconfigpkgloadplyrpraiseprocessxpromisespsR6rappdirsRColorBrewerRcpprematch2reshape2RhtslibrlangrprojrootRsamtoolsS4VectorssassscalesshinyshinyFilesshinyjssnowsourcetoolsstringistringrsystestthattibbleUCSC.utilsutf8vctrsviridisLitewaldowithrxtableXVectorzipzlibbioc