CENTREannotation
This is the development version of CENTREannotation; for the stable release version, see CENTREannotation.
Hub package for the annotation data of CENTRE (GENCODE v40 and SCREEN v3)
Bioconductor version: Development (3.24)
This is an AnnotationHub package for the CENTRE Bioconductor software package. It contains the GENCODE version 40 annotation and ENCODE Registry of candidate cis-regulatory elements (cCREs) version 3. All for Human hg38 genome.
Author: Sara Lopez Ruiz de Vargas [aut, cre]
Maintainer: Sara Lopez Ruiz de Vargas <lopez_s at molgen.mpg.de>
citation("CENTREannotation")):
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("CENTREannotation")
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("CENTREannotation")| CENTRE AnnotationHub datasets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AnnotationData, AnnotationHub |
| Version | 0.99.1 |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | AnnotationHub, RSQLite, DBI, BiocGenerics, methods |
| System Requirements | |
| URL | https://github.com/slrvv/CENTREannotation |
| Bug Reports | https://github.com/slrvv/CENTREannotation/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CENTREannotation_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/CENTREannotation/ |
| Package Downloads Report | Download Stats |