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:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=PlasmaMutationDetector2
to link to this page.