MADSEQ
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MADSEQ.
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Bioconductor version: 3.11
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("MADSEQ")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 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 |
| System Requirements | |
| URL | https://github.com/ykong2/MADSEQ |
| Bug Reports | https://github.com/ykong2/MADSEQ/issues |
See More
| Suggests | knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MADSEQ_1.14.0.tar.gz |
| Windows Binary | MADSEQ_1.14.0.zip |
| macOS 10.13 (High Sierra) | MADSEQ_1.14.0.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 3.11 | Source Archive |