Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

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Documentation for package ‘BgeeDB’ version 2.31.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Bgee	Bgee Reference Class
Bgee-class	Bgee Reference Class
deleteLocalData	Delete local data for the species of the reference class Bgee object
deleteOldData	Delete .rds data of one species coming from an old version of the BgeeDB R package.
formatData	Format RNA-seq or Affymetrix data downloaded from Bgee.
geneList	Example of gene list object used to run a topAnat enrichment test, created on June 2018. The format of the gene list is the same as the gene list required to build a 'topGOdata' object in the 'topGO' package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. In this example the foreground genes are zebrafish genes with an annotated phenotype related to "pectoral fin", and the background is composed of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. The gene list was built using the biomaRt package, and the code used can be found in the vignette of the package.
getAnnotation	Retrieve Bgee experiments annotation for targeted species and data type.
getData	Retrieve Bgee RNA-seq or Affymetrix data.
listBgeeRelease	List Bgee releases available to use with BgeeDB package
listBgeeSpecies	List species in the Bgee database and the available data types for each of them
loadTopAnatData	Retrieve data from Bgee to perform GO-like enrichment of anatomical terms, mapped to genes by expression patterns.
makeTable	Formats results of the enrichment test on anatomical structures.
topAnat	Produces an object allowing to perform GO-like enrichment of anatomical terms using the topGO package