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.

AuthorYves Rozenholc, Nicolas P├ęcuchet, Pierre Laurent-Puig
Date of publication2016-09-09 10:13:42
MaintainerYves Rozenholc <yves.rozenholc@parisdescartes.fr>
LicenseMIT + file LICENSE
Version1.5.2

View on CRAN

Files in this package

PlasmaMutationDetector
PlasmaMutationDetector/inst
PlasmaMutationDetector/inst/extdata
PlasmaMutationDetector/inst/extdata/4test_only
PlasmaMutationDetector/inst/extdata/4test_only/case
PlasmaMutationDetector/inst/extdata/4test_only/case/rBAM
PlasmaMutationDetector/inst/extdata/4test_only/case/rBAM/case1.chr7.bam
PlasmaMutationDetector/inst/extdata/4test_only/case/rBAM/case1.chr7.bam.bai
PlasmaMutationDetector/inst/extdata/4test_only/case/BER
PlasmaMutationDetector/inst/extdata/4test_only/case/BER/case1.chr7_MAF.txt
PlasmaMutationDetector/inst/extdata/4test_only/ctrl
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/rBAM
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/rBAM/ctrl1-downsample-05.bam.bai
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/rBAM/ctrl1-downsample-05.bam
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/BER
PlasmaMutationDetector/inst/extdata/4test_only/ctrl/BER/ctrl1-downsample-05_MAF.txt.zip
PlasmaMutationDetector/inst/extdata/Info
PlasmaMutationDetector/inst/extdata/Info/lungcolonV2.bed.txt
PlasmaMutationDetector/NAMESPACE
PlasmaMutationDetector/data
PlasmaMutationDetector/data/positions_ranges.rda
PlasmaMutationDetector/data/hotspot.txt.gz
PlasmaMutationDetector/data/background_error_rate.txt.gz
PlasmaMutationDetector/R
PlasmaMutationDetector/R/functions.R
PlasmaMutationDetector/MD5
PlasmaMutationDetector/DESCRIPTION
PlasmaMutationDetector/man
PlasmaMutationDetector/man/positions_ranges.Rd PlasmaMutationDetector/man/MAF_from_BAM.Rd PlasmaMutationDetector/man/background_error_rate.Rd PlasmaMutationDetector/man/hotspot.Rd PlasmaMutationDetector/man/DetectPlasmaMutation.Rd PlasmaMutationDetector/man/BuildCtrlErrorRate.Rd PlasmaMutationDetector/man/PrepareLibrary.Rd
PlasmaMutationDetector/LICENSE

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