Package: CNVPanelizer 1.45.0
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_1.45.0.tar.gz
CNVPanelizer_1.45.0.zip(r-4.7)CNVPanelizer_1.45.0.zip(r-4.6)CNVPanelizer_1.45.0.zip(r-4.5)
CNVPanelizer_1.45.0.tgz(r-4.6-any)CNVPanelizer_1.45.0.tgz(r-4.5-any)
CNVPanelizer_1.45.0.tar.gz(r-4.7-any)CNVPanelizer_1.45.0.tar.gz(r-4.6-any)
CNVPanelizer_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.45.0(bioc 3.24)CNVPanelizer-1.44.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationsequencingnormalizationcopynumbervariationcoverage
Last updated from:f1d71f9de0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 181 | ||
| linux-devel-x86_64 | NOTE | 390 | ||
| source / vignettes | OK | 348 | ||
| linux-release-x86_64 | NOTE | 324 | ||
| macos-release-arm64 | NOTE | 165 | ||
| macos-oldrel-arm64 | NOTE | 167 | ||
| windows-devel | NOTE | 248 | ||
| windows-release | NOTE | 224 | ||
| windows-oldrel | NOTE | 243 | ||
| wasm-release | OK | 140 |
Exports:BackgroundBedToGenomicRangesBootListCNVPanelizerCNVPanelizerFromReadCountsCNVPanelizerFromReadCountsHELPERCollectColumnFromAllReportTablesCombinedNormalizedCountsIndexMultipleBamsNormalizeCountsPlotBootstrapDistributionsReadCountsFromBamReadXLSXToListReportTablesRunCNVPanelizerShinySelectReferenceSetByInterquartileRangeSelectReferenceSetByKmeansSelectReferenceSetByPercentilSelectReferenceSetFromReadCountsStatusHeatmapWriteListToXLSX
Dependencies:askpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbriobslibcachemcallrcaToolsclicodetoolscommonmarkcpp11crayoncurldescdiffobjdigestevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicRangesggplot2gluegplotsgtablegtoolshtmltoolshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothlabelinglambda.rlaterlatticelifecyclemagrittrMatrixmemoisemimeNOISeqopensslopenxlsxotelpillarpkgbuildpkgconfigpkgloadplyrpraiseprocessxpromisespsR6rappdirsRColorBrewerRcppreshape2RhtslibrlangrprojrootRsamtoolsS4VectorsS7sassscalesSeqinfoshinyshinyFilesshinyjssnowsourcetoolsstringistringrsystestthattibbleUCSC.utilsutf8vctrsviridisLitewaldowithrxtableXVectorzip
