PlasmaMutationDetector: Tumor Mutation Detection in Plasma

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. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.

Version: 1.6.10
Depends: R (≥ 3.4.0), 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: 2018-01-26
Author: Yves Rozenholc, Nicolas P├ęcuchet, Pierre Laurent-Puig
Maintainer: Yves Rozenholc <yves.rozenholc at>
License: MIT + file LICENSE
NeedsCompilation: no
CRAN checks: PlasmaMutationDetector results


Reference manual: PlasmaMutationDetector.pdf
Package source: PlasmaMutationDetector_1.6.10.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X El Capitan binaries: r-release: PlasmaMutationDetector_1.6.10.tgz
OS X Mavericks binaries: r-oldrel: not available
Old sources: PlasmaMutationDetector archive


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