MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MADSEQ")
AuthorYu Kong, Adam Auton, John Murray Greally
Bioconductor views Bayesian CopyNumberVariation Coverage GenomicVariation Sequencing SomaticMutation VariantDetection
Date of publicationNone
MaintainerYu Kong <yu.kong@phd.einstein.yu.edu>
LicenseGPL(>=2)
Version1.0.0
https://github.com/ykong2/MADSEQ

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/MADSEQ.R R/MadSeqMethod.R R/PlotHelper.R R/PlotShow.R R/PreProcessingHelper.R R/PreProcessingShow.R R/RunModelHelper.R R/RunModelShow.R R/data.R
README.md
build
build/vignette.rds
data
data/aneuploidy_chr18.RData
inst
inst/NEWS
inst/doc
inst/doc/MADSEQ-vignette.R
inst/doc/MADSEQ-vignette.Rmd
inst/doc/MADSEQ-vignette.html
inst/extdata
inst/extdata/aneuploidy.bam
inst/extdata/aneuploidy.bam.bai
inst/extdata/aneuploidy.vcf.gz
inst/extdata/aneuploidy.vcf1.gz
inst/extdata/normal.bam
inst/extdata/normal.bam.bai
inst/extdata/normal.vcf.gz
inst/extdata/target.bed
inst/rjags
inst/rjags/FourMix.txt
inst/rjags/LOH.txt
inst/rjags/OneMix.txt
inst/rjags/TwoMixMonosomy.txt
inst/rjags/TwoMixTrisomy.txt
man
man/MADSEQ-package.Rd man/MadSeq.Rd man/aneuploidy_chr18.Rd man/deltaBIC.Rd man/normalizeCoverage.Rd man/plotFraction.Rd man/plotMadSeq.Rd man/plotMixture.Rd man/posterior.Rd man/prepareCoverageGC.Rd man/prepareHetero.Rd man/runMadSeq.Rd man/summary-method.Rd
vignettes
vignettes/MADSEQ-vignette.Rmd

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