Package: PlasmaMutationDetector2
Type: Package
Title: Tumor Mutation Detection in Plasma using Barcoding
Version: 1.1.11
Date: 2022-04-07
Author: Yves Rozenholc [cre, aut]
	Oddmund Nordgård [con, aut]
	Nicolas Pécuchet [con]
	Pierre-Laurent Puig [con]
Maintainer: Rozenholc <yves.rozenholc@u-paris.fr>
Description: 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>.
License: MIT + file LICENSE
Imports: S4Vectors (>= 0.16.0), Rsamtools (>= 1.30.0), rtracklayer (>=
        1.38.0), robustbase (>= 0.92-8), SummarizedExperiment (>=
        1.8.0)
Depends: R (>= 3.5.0), ggplot2 (>= 2.2.0), grid (>= 3.4.0),
        GenomicRanges (>= 1.30.0), VariantAnnotation (>= 1.24.0)
Encoding: UTF-8
RoxygenNote: 7.1.2
LazyData: true
NeedsCompilation: no
Packaged: 2022-04-29 11:04:34 UTC; rozen
Repository: CRAN
Date/Publication: 2022-05-03 10:00:08 UTC
Built: R 4.1.3; ; 2023-04-17 17:08:23 UTC; windows
