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.

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Description file content

Package
PlasmaMutationDetector
Type
Package
Title
Tumor Mutation Detection in Plasma
Version
1.7.2
Date
2018-05-16
Author
Yves Rozenholc, Nicolas Pécuchet, Pierre Laurent-Puig
Maintainer
Yves Rozenholc
Description
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.
License
MIT + file LICENSE
Imports
S4Vectors (>= 0.16.0), Rsamtools (>= 1.30.0), rtracklayer (>= 1.38.0), robustbase (>= 0.92-8), SummarizedExperiment (>= 1.8.0)
Depends
R (>= 3.4.0), ggplot2 (>= 2.2.0), grid (>= 3.4.0), GenomicRanges (>= 1.30.0), VariantAnnotation (>= 1.24.0)
Encoding
UTF-8
RoxygenNote
6.0.1
LazyData
true
NeedsCompilation
no
Packaged
2018-06-11 02:11:42 UTC; rozen
Repository
CRAN
Date/Publication
2018-06-11 07:43:09 UTC

install.packages('PlasmaMutationDetector')

1.7.2

9 days ago

Yves Rozenholc

MIT + file LICENSE

Depends on

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)

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