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:Cristiano Oliveira [aut], Thomas Wolf [aut, cre], Albrecht Stenzinger [ctb], Volker Endris [ctb], Nicole Pfarr [ctb], Benedikt Brors [ths], Wilko Weichert [ths]

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✨
DESCRIPTION |NEWS
card.svg |card.png
CNVPanelizer/json (API)

# Install 'CNVPanelizer' in R:

install.packages('CNVPanelizer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

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.

classification sequencing normalization copynumbervariation coverage

4.92 score 12 scripts 7 mentions 21 exports 103 dependencies

Last updated from:f1d71f9de0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	185
linux-devel-x86_64	NOTE	296
source / vignettes	OK	269
linux-release-x86_64	NOTE	290
macos-release-arm64	NOTE	152
macos-oldrel-arm64	NOTE	154
windows-devel	NOTE	212
windows-release	NOTE	229
windows-oldrel	NOTE	201
wasm-release	OK	181

Exports:Background BedToGenomicRanges BootList CNVPanelizer CNVPanelizerFromReadCounts CNVPanelizerFromReadCountsHELPER CollectColumnFromAllReportTables CombinedNormalizedCounts IndexMultipleBams NormalizeCounts PlotBootstrapDistributions ReadCountsFromBam ReadXLSXToList ReportTables RunCNVPanelizerShiny SelectReferenceSetByInterquartileRange SelectReferenceSetByKmeans SelectReferenceSetByPercentil SelectReferenceSetFromReadCounts StatusHeatmap WriteListToXLSX

Dependencies:askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bitops brio bslib cachem callr caTools cli codetools commonmark cpp11 crayon curl desc diffobj digest evaluate farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomicRanges ggplot2 glue gplots gtable gtools htmltools httpuv httr IRanges isoband iterators jquerylib jsonlite KernSmooth labeling lambda.r later lattice lifecycle magrittr Matrix memoise mime NOISeq openssl openxlsx otel pillar pkgbuild pkgconfig pkgload plyr praise processx promises ps R6 rappdirs RColorBrewer Rcpp reshape2 Rhtslib rlang rprojroot Rsamtools S4Vectors S7 sass scales Seqinfo shiny shinyFiles shinyjs snow sourcetools stringi stringr sys testthat tibble UCSC.utils utf8 vctrs viridisLite waldo withr xtable XVector zip

CNVPanelizer

Introduction | Using

Rendered fromCNVPanelizer.Rnwusingknitr::knitr

Last update: 2018-08-30
Started: 2015-06-25

Help page	Topics
Reliable CNV detection in targeted sequencing applications	CNVPanelizer-package CNVPanelizer
Background	Background
BedToGenomicRanges	BedToGenomicRanges
BootList	BootList
CNVPanelizerFromReadCounts	CNVPanelizerFromReadCounts
CNVPanelizerFromReadCountsHELPER	CNVPanelizerFromReadCountsHELPER
CollectColumnFromAllReportTables	CollectColumnFromAllReportTables
CombinedNormalizedCounts	CombinedNormalizedCounts
IndexMultipleBams	IndexMultipleBams
NormalizeCounts	NormalizeCounts
PlotBootstrapDistributions	PlotBootstrapDistributions
ReadCountsFromBam	ReadCountsFromBam
ReadXLSXToList	ReadXLSXToList
Reference sample data	referenceReadCounts
ReportTables	ReportTables
RunCNVPanelizerShiny	RunCNVPanelizerShiny
Test sample data	sampleReadCounts
SelectReferenceSetByInterquartileRange	SelectReferenceSetByInterquartileRange
SelectReferenceSetByKmeans	SelectReferenceSetByKmeans
SelectReferenceSetByPercentil	SelectReferenceSetByPercentil
SelectReferenceSetFromReadCounts	SelectReferenceSetFromReadCounts
StatusHeatmap	StatusHeatmap
WriteListToXLSX	WriteListToXLSX

Package: CNVPanelizer 1.45.0

CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)