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: 1.6.2
Depends: R (≥ 3.3.1), ggplot2 (≥ 2.0.0), grid (≥ 3.2.3), GenomicRanges (≥ 1.22.3), VariantAnnotation (≥ 1.16.4)
Imports: S4Vectors (≥ 0.8.7), Rsamtools (≥ 1.22.0), rtracklayer (≥ 1.30.1), robustbase (≥ 0.92-5), SummarizedExperiment (≥ 1.2.3)
Published: 2017-11-15
Author: Yves Rozenholc, Nicolas P├ęcuchet, Pierre Laurent-Puig
Maintainer: Yves Rozenholc <yves.rozenholc at parisdescartes.fr>
License: MIT + file LICENSE
NeedsCompilation: no
CRAN checks: PlasmaMutationDetector results

Downloads:

Reference manual: PlasmaMutationDetector.pdf
Package source: PlasmaMutationDetector_1.6.2.tar.gz
Windows binaries: r-devel: PlasmaMutationDetector_1.6.2.zip, r-release: PlasmaMutationDetector_1.6.2.zip, r-oldrel: PlasmaMutationDetector_1.6.2.zip
OS X El Capitan binaries: r-release: not available
OS X Mavericks binaries: r-oldrel: not available
Old sources: PlasmaMutationDetector archive

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