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.

AuthorYu Kong, Adam Auton, John Murray Greally
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 in this package

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

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