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>

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

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")

 

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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

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