MADSEQ

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MADSEQ.

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Bioconductor version: 3.15

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 "4.2") and enter:


if (!require("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")

R Package MADSEQ HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection

Version 1.22.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 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

System Requirements

URL https://github.com/ykong2/MADSEQ

Bug Reports https://github.com/ykong2/MADSEQ/issues

Suggests knitr

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Build Report Build Report

Package Archives

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

Source Package MADSEQ_1.22.0.tar.gz

Windows Binary MADSEQ_1.22.0.zip

macOS Binary (x86_64) MADSEQ_1.22.0.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

Old Source Packages for BioC 3.15 Source Archive