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.


Reference manual

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1.5.2 by Yves Rozenholc, a year ago

Browse source code at https://github.com/cran/PlasmaMutationDetector

Authors: Yves Rozenholc, Nicolas P├ęcuchet, Pierre Laurent-Puig

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports S4Vectors, Rsamtools, rtracklayer, robustbase, SummarizedExperiment

Depends on ggplot2, grid, GenomicRanges, VariantAnnotation

See at CRAN