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MADSEQ

This is the development version of MADSEQ; for the stable release version, see MADSEQ.

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
R Package MADSEQ HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection
Version 1.27.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License GPL(>=2)
Depends R (>= 3.5.0), 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
Linking To
Suggests knitr
System Requirements
Enhances
URL https://github.com/ykong2/MADSEQ
Bug Reports https://github.com/ykong2/MADSEQ/issues
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Package Archives

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

Source Package MADSEQ_1.27.0.tar.gz
Windows Binary MADSEQ_1.27.0.zip
macOS Binary (x86_64) MADSEQ_1.27.0.tgz
macOS Binary (arm64) MADSEQ_1.27.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MADSEQ
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MADSEQ
Bioc Package Browser https://code.bioconductor.org/browse/MADSEQ/
Package Short Url https://bioconductor.org/packages/MADSEQ/
Package Downloads Report Download Stats