MADSEQ

DOI: 10.18129/B9.bioc.MADSEQ    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MADSEQ.

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MADSEQ")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MADSEQ")

 

HTML	R Script	R Package MADSEQ
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
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, vcfR
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
Links To Me
Build Report

Package Archives

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

Source Package	MADSEQ_1.8.0.tar.gz
Windows Binary	MADSEQ_1.8.0.zip
Mac OS X 10.11 (El Capitan)	MADSEQ_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MADSEQ
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MADSEQ
Package Short Url	http://bioconductor.org/packages/MADSEQ/
Package Downloads Report	Download Stats