Package: BgeeDB 2.31.0

Julien Wollbrett

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

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.

Authors:Andrea Komljenovic [aut, cre], Julien Roux [aut, cre]

BgeeDB_2.31.0.tar.gz
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BgeeDB.pdf |BgeeDB.html✨
BgeeDB/json (API)
NEWS

# Install 'BgeeDB' in R:
install.packages('BgeeDB', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bgeedb/bgeedb_r/issues

Datasets:
  • 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.

On BioConductor:BgeeDB-2.31.0(bioc 3.20)BgeeDB-2.30.0(bioc 3.19)

bioconductor-package

11 exports 2.31 score 64 dependencies 2 dependents 4 mentions

Last updated 2 months agofrom:b559d69b78

Exports:BgeedeleteLocalDatadeleteOldDataformatDatagetAnnotationgetDatalistBgeeReleaselistBgeeSpeciesloadTopAnatDatamakeTabletopAnat

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicpp11crayoncurldata.tableDBIdigestdplyrfansifastmapgenericsGenomeInfoDbGenomeInfoDbDataglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlatticelifecyclemagrittrmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpurrrR.methodsS3R.ooR.utilsR6RCurlrlangRSQLiteS4VectorsSparseMstringistringrsystibbletidyrtidyselecttopGOUCSC.utilsutf8vctrswithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Bgee Reference ClassBgee Bgee-class
Delete local data for the species of the reference class Bgee objectdeleteLocalData
Delete .rds data of one species coming from an old version of the BgeeDB R package.deleteOldData
Format RNA-seq or Affymetrix data downloaded from Bgee.formatData
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.geneList
Retrieve Bgee experiments annotation for targeted species and data type.getAnnotation
Retrieve Bgee RNA-seq or Affymetrix data.getData
List Bgee releases available to use with BgeeDB packagelistBgeeRelease
List species in the Bgee database and the available data types for each of themlistBgeeSpecies
Retrieve data from Bgee to perform GO-like enrichment of anatomical terms, mapped to genes by expression patterns.loadTopAnatData
Formats results of the enrichment test on anatomical structures.makeTable
Produces an object allowing to perform GO-like enrichment of anatomical terms using the topGO packagetopAnat