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.

Install the latest version of this package by entering the following in R:
install.packages("PlasmaMutationDetector")
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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