BgeeDB
This is the released version of BgeeDB; for the devel version, see BgeeDB.
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Bioconductor version: Release (3.23)
A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.
Author: Andrea Komljenovic [aut, cre], Julien Roux [aut, cre]
Maintainer: Julien Wollbrett <julien.wollbrett at unil.ch>, Julien Roux <julien.roux at unibas.ch>, Andrea Komljenovic <andreakomljenovic at gmail.com>, Frederic Bastian <bgee at sib.swiss>
citation("BgeeDB")):
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("BgeeDB")
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("BgeeDB")| BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software |
| Version | 2.38.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 3.6.0), topGO, tidyr |
| Imports | R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata, HDF5Array, bread |
| System Requirements | |
| URL | https://github.com/BgeeDB/BgeeDB_R |
| Bug Reports | https://github.com/BgeeDB/BgeeDB_R/issues |
See More
| Suggests | knitr, BiocStyle, testthat, rmarkdown, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | RITAN |
| Suggests Me | RITAN |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BgeeDB_2.38.1.tar.gz |
| Windows Binary (x86_64) | BgeeDB_2.38.1.zip |
| macOS Binary (big-sur-x86_64) | BgeeDB_2.38.1.tgz |
| macOS Binary (sonoma-arm64) | BgeeDB_2.38.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BgeeDB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BgeeDB |
| Bioc Package Browser | https://code.bioconductor.org/browse/BgeeDB/ |
| Package Short Url | https://bioconductor.org/packages/BgeeDB/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |