biomvRCNS
This is the development version of biomvRCNS; for the stable release version, see biomvRCNS.
Copy Number study and Segmentation for multivariate biological data
Bioconductor version: Development (3.24)
In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.
Author: Yang Du
Maintainer: Yang Du <tooyoung at gmail.com>
citation("biomvRCNS")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("biomvRCNS")
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("biomvRCNS")| biomvRCNS package introduction | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Genetics, Microarray, Sequencing, Software, Visualization, aCGH |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL (>= 2) |
| Depends | IRanges, GenomicRanges, Gviz |
| Imports | methods, mvtnorm |
| System Requirements | |
| URL |
See More
| Suggests | cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene |
| 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 | biomvRCNS_1.53.0.tar.gz |
| Windows Binary (x86_64) | biomvRCNS_1.53.0.zip |
| macOS Binary (big-sur-x86_64) | biomvRCNS_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | biomvRCNS_1.53.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/biomvRCNS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/biomvRCNS |
| Bioc Package Browser | https://code.bioconductor.org/browse/biomvRCNS/ |
| Package Short Url | https://bioconductor.org/packages/biomvRCNS/ |
| Package Downloads Report | Download Stats |