BgeeDB
This is thereleased version of BgeeDB; for the devel version, seeBgeeDB.
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("BgeeDB")For older versions of R, please refer to the appropriateBioconductor 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 | 2.36.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (9.5 years) |
| License | GPL-3 + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | BgeeDB_2.36.0.tar.gz |
| Windows Binary (x86_64) | BgeeDB_2.36.0.zip |
| macOS Binary (x86_64) | BgeeDB_2.36.0.tgz |
| macOS Binary (arm64) | BgeeDB_2.36.0.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 |