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 |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
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Installation instructions to use this
package in your R session.
Read more here: Source link
