To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MADSEQ")

In most cases, you don't need to download the package archive at all.

MADSEQ

DOI: 10.18129/B9.bioc.MADSEQ    

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Bioconductor version: Release (3.6)

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.

Author: Yu Kong, Adam Auton, John Murray Greally

Maintainer: Yu Kong <yu.kong at phd.einstein.yu.edu>

Citation (from within R, enter citation("MADSEQ")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MADSEQ")

Documentation

HTML R Script R Package MADSEQ
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection
Version 1.4.1
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL(>=2)
Depends R (>= 3.4), rjags (>= 4-6)
Imports VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL https://github.com/ykong2/MADSEQ
BugReports https://github.com/ykong2/MADSEQ/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MADSEQ_1.4.1.tar.gz
Windows Binary MADSEQ_1.4.1.zip
Mac OS X 10.11 (El Capitan) MADSEQ_1.4.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MADSEQ
Package Short Url http://bioconductor.org/packages/MADSEQ/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: