nuCpos
This is the development version of nuCpos; for the stable release version, see nuCpos.
An R package for prediction of nucleosome positions
Bioconductor version: Development (3.24)
nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.
Author: Hiroaki Kato, Takeshi Urano
Maintainer: Hiroaki Kato <hkato at med.shimane-u.ac.jp>
citation("nuCpos")):
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("nuCpos")
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("nuCpos")| An R package for prediction of nucleosome positioning | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Epigenetics, Genetics, NucleosomePositioning, Software |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-2 |
| Depends | R (>= 4.2.0) |
| Imports | graphics, methods |
| System Requirements | |
| URL |
See More
| Suggests | NuPoP, Biostrings, testthat |
| 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 | nuCpos_1.31.0.tar.gz |
| Windows Binary (x86_64) | nuCpos_1.31.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | nuCpos_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | nuCpos_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/nuCpos |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nuCpos |
| Bioc Package Browser | https://code.bioconductor.org/browse/nuCpos/ |
| Package Short Url | https://bioconductor.org/packages/nuCpos/ |
| Package Downloads Report | Download Stats |