PlasmaMutationDetector2: Tumor Mutation Detection in Plasma using Barcoding

Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis using barcoding. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples. This package has been used for Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) <https://www.nature.com/articles/s41598-022-09698-5>.

Version:	1.1.11
Depends:	R (≥ 3.5.0), ggplot2 (≥ 2.2.0), grid (≥ 3.4.0), GenomicRanges (≥ 1.30.0), VariantAnnotation (≥ 1.24.0)
Imports:	S4Vectors (≥ 0.16.0), Rsamtools (≥ 1.30.0), rtracklayer (≥ 1.38.0), robustbase (≥ 0.92-8), SummarizedExperiment (≥ 1.8.0)
Published:	2022-05-03
DOI:	10.32614/CRAN.package.PlasmaMutationDetector2
Author:	Yves Rozenholc [cre, aut] Oddmund Nordgård [con, aut] Nicolas Pécuchet [con] Pierre-Laurent Puig [con]
Maintainer:	Rozenholc <yves.rozenholc at u-paris.fr>
License:	MIT + file LICENSE
NeedsCompilation:	no
CRAN checks:	PlasmaMutationDetector2 results

Documentation:

Reference manual:

PlasmaMutationDetector2.pdf

Downloads:

Package source:	PlasmaMutationDetector2_1.1.11.tar.gz
Windows binaries:	r-devel: PlasmaMutationDetector2_1.1.11.zip, r-release: PlasmaMutationDetector2_1.1.11.zip, r-oldrel: PlasmaMutationDetector2_1.1.11.zip
macOS binaries:	r-release (arm64): PlasmaMutationDetector2_1.1.11.tgz, r-oldrel (arm64): PlasmaMutationDetector2_1.1.11.tgz, r-release (x86_64): PlasmaMutationDetector2_1.1.11.tgz, r-oldrel (x86_64): PlasmaMutationDetector2_1.1.11.tgz

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