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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: | 1.7.2 |
| 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: | 2018-06-11 |
| DOI: | 10.32614/CRAN.package.PlasmaMutationDetector |
| Author: | Yves Rozenholc, Nicolas Pécuchet, Pierre Laurent-Puig |
| Maintainer: | Yves Rozenholc <yves.rozenholc at parisdescartes.fr> |
| License: | MIT + file LICENSE |
| NeedsCompilation: | no |
| CRAN checks: | PlasmaMutationDetector results |
| Reference manual: | PlasmaMutationDetector.pdf |
| Package source: | PlasmaMutationDetector_1.7.2.tar.gz |
| Windows binaries: | r-devel: PlasmaMutationDetector_1.7.2.zip, r-release: PlasmaMutationDetector_1.7.2.zip, r-oldrel: PlasmaMutationDetector_1.7.2.zip |
| macOS binaries: | r-release (arm64): PlasmaMutationDetector_1.7.2.tgz, r-oldrel (arm64): PlasmaMutationDetector_1.7.2.tgz, r-release (x86_64): PlasmaMutationDetector_1.7.2.tgz, r-oldrel (x86_64): PlasmaMutationDetector_1.7.2.tgz |
| Old sources: | PlasmaMutationDetector archive |
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