RCNA: Robust Copy Number Alteration Detection (RCNA)

Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.

Version:	1.0
Depends:	R (≥ 3.5.0)
Imports:	doParallel, methods, utils, modeest, data.table, foreach, R.utils
Suggests:	knitr, rmarkdown, usethis
Published:	2024-12-03
DOI:	10.32614/CRAN.package.RCNA
Author:	Matt Bradley [aut, cre]
Maintainer:	Matt Bradley <mbradley at emmes.com>
License:	GPL-3
NeedsCompilation:	no
Materials:	README NEWS
CRAN checks:	RCNA results

Documentation:

Reference manual:	RCNA.pdf
Vignettes:	Detecting Copy Number Variation on Targeted Exon Sequencing with RCNA (source)

Downloads:

Package source:	RCNA_1.0.tar.gz
Windows binaries:	r-devel: RCNA_1.0.zip, r-release: RCNA_1.0.zip, r-oldrel: RCNA_1.0.zip
macOS binaries:	r-release (arm64): RCNA_1.0.tgz, r-oldrel (arm64): RCNA_1.0.tgz, r-release (x86_64): RCNA_1.0.tgz, r-oldrel (x86_64): RCNA_1.0.tgz

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