To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MADSEQ")
In most cases, you don't need to download the package archive at all.
MADSEQ
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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MADSEQ.
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Bioconductor version: 3.4
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MADSEQ")
Documentation
| HTML | R Script | R Package MADSEQ |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, CopyNumberVariation, Coverage, GenomicVariation, Sequencing, Software, SomaticMutation, VariantDetection |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 years) |
| License | GPL(>=2) |
| Depends | R (>= 3.3), 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 |
| LinkingTo | |
| Suggests | knitr |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/ykong2/MADSEQ |
| BugReports | https://github.com/ykong2/MADSEQ/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MADSEQ_1.0.0.tar.gz |
| Windows Binary | MADSEQ_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | MADSEQ_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/MADSEQ/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/MADSEQ/ |
| Package Downloads Report | Download Stats |
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