BgeeDB
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") 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 | 2.32.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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_2.32.0.tar.gz |
| Windows Binary (x86_64) | BgeeDB_2.32.0.zip |
| macOS Binary (x86_64) | BgeeDB_2.32.0.tgz |
| macOS Binary (arm64) | BgeeDB_2.32.0.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 3.20 | Source Archive |