CENTREprecomputed
This is the released version of CENTREprecomputed; for the devel version, see CENTREprecomputed.
Hub package for the precomputed data of CENTRE and example data
Bioconductor version: Release (3.23)
Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package.
Author: Sara Lopez Ruiz de Vargas [aut, cre]
Maintainer: Sara Lopez Ruiz de Vargas <lopez_s at molgen.mpg.de>
citation("CENTREprecomputed")):
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")
BiocManager::install("CENTREprecomputed")
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("CENTREprecomputed")| CENTRE ExperimentHub datasets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeqData, ChipOnChipData, ExperimentData, ExperimentHub, PackageTypeData, RNASeqData |
| Version | 1.2.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | ExperimentHub, RSQLite, DBI, BiocGenerics, methods |
| System Requirements | |
| URL | https://github.com/slrvv/CENTREprecomputed |
| Bug Reports | https://github.com/slrvv/CENTREprecomputed/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| 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 | CENTREprecomputed_1.2.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CENTREprecomputed |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CENTREprecomputed |
| Package Short Url | https://bioconductor.org/packages/CENTREprecomputed/ |
| Package Downloads Report | Download Stats |