Bioconductor – MADSEQ

DOI: 10.18129/B9.bioc.MADSEQ  

 

This package is for version 3.10 of Bioconductor;
for the stable, up-to-date release version, see
MADSEQ.

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Bioconductor version: 3.10

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
“3.6”) 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")

 

Details

biocViews Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection
Version 1.12.0
In Bioconductor since BioC 3.4 (R-3.3) (3.5 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 github.com/ykong2/MADSEQ
BugReports github.com/ykong2/MADSEQ/issues
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Installation
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package in your R session.


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