Package: CNVPanelizer 1.39.0
Thomas Wolf
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.
Authors:
CNVPanelizer_1.39.0.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-1.39.0(bioc 3.21)CNVPanelizer-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationsequencingnormalizationcopynumbervariationcoverage
Last updated 2 months agofrom:4aac16fafd. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 14 2024 |
| R-4.5-win | NOTE | Dec 14 2024 |
| R-4.5-linux | NOTE | Dec 14 2024 |
| R-4.4-win | NOTE | Dec 14 2024 |
| R-4.4-mac | NOTE | Dec 14 2024 |
| R-4.3-win | NOTE | Dec 14 2024 |
| R-4.3-mac | NOTE | Dec 14 2024 |
Exports:BackgroundBedToGenomicRangesBootListCNVPanelizerCNVPanelizerFromReadCountsCNVPanelizerFromReadCountsHELPERCollectColumnFromAllReportTablesCombinedNormalizedCountsIndexMultipleBamsNormalizeCountsPlotBootstrapDistributionsReadCountsFromBamReadXLSXToListReportTablesRunCNVPanelizerShinySelectReferenceSetByInterquartileRangeSelectReferenceSetByKmeansSelectReferenceSetByPercentilSelectReferenceSetFromReadCountsStatusHeatmapWriteListToXLSX
Dependencies:askpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbriobslibcachemcallrcaToolsclicodetoolscolorspacecommonmarkcpp11crayoncurldescdiffobjdigestevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshtmltoolshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothlabelinglambda.rlaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeNOISeqopensslopenxlsxpillarpkgbuildpkgconfigpkgloadplyrpraiseprocessxpromisespsR6rappdirsRColorBrewerRcppreshape2RhtslibrlangrprojrootRsamtoolsS4VectorssassscalesshinyshinyFilesshinyjssnowsourcetoolsstringistringrsystestthattibbleUCSC.utilsutf8vctrsviridisLitewaldowithrxtableXVectorzipzlibbioc
