BgeeDB: Annotation and gene expression data retrieval from Bgee database

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]
Date of publication
None
Maintainer
Andrea Komljenovic <andreakomljenovic@gmail.com>, Frederic Bastian <bgee@sib.swiss>
License
GPL-2
Version
2.0.0

View on Bioconductor

Man pages

Bgee-class
Bgee Reference Class
formatData
Format RNA-seq or Affymetrix data downloaded from Bgee.
getAnnotation
Retrieve Bgee experiments annotation for targeted species and...
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...
loadTopAnatData
Retrieve data from Bgee to perform GO-like enrichment of...
makeTable
Formats results of the enrichment test on anatomical...
topAnat
Produces an object allowing to perform GO-like enrichment of...

Files in this package

BgeeDB/DESCRIPTION
BgeeDB/NAMESPACE
BgeeDB/NEWS
BgeeDB/R
BgeeDB/R/Bgee.R
BgeeDB/R/formatData.R
BgeeDB/R/getAnnotation.R
BgeeDB/R/getData.R
BgeeDB/R/listBgeeRelease.R
BgeeDB/R/listBgeeSpecies.R
BgeeDB/R/loadTopAnatData.R
BgeeDB/R/makeTable.R
BgeeDB/R/topAnat.R
BgeeDB/README.md
BgeeDB/build
BgeeDB/build/vignette.rds
BgeeDB/inst
BgeeDB/inst/CITATION
BgeeDB/inst/NEWS.Rd
BgeeDB/inst/doc
BgeeDB/inst/doc/BgeeDB_Manual.R
BgeeDB/inst/doc/BgeeDB_Manual.Rmd
BgeeDB/inst/doc/BgeeDB_Manual.html
BgeeDB/man
BgeeDB/man/Bgee-class.Rd
BgeeDB/man/formatData.Rd
BgeeDB/man/getAnnotation.Rd
BgeeDB/man/getData.Rd
BgeeDB/man/listBgeeRelease.Rd
BgeeDB/man/listBgeeSpecies.Rd
BgeeDB/man/loadTopAnatData.Rd
BgeeDB/man/makeTable.Rd
BgeeDB/man/topAnat.Rd
BgeeDB/tests
BgeeDB/tests/testthat
BgeeDB/tests/testthat.R
BgeeDB/tests/testthat/test_format_data.R
BgeeDB/tests/testthat/test_list_annotation_output.R
BgeeDB/tests/testthat/test_listspecies_output.R
BgeeDB/tests/testthat/test_loadTopAnatData.R
BgeeDB/tests/testthat/test_loading_data_Bgee.R
BgeeDB/tests/testthat/test_loading_separate_experiment.R
BgeeDB/tests/testthat/test_topAnat.R
BgeeDB/vignettes
BgeeDB/vignettes/BgeeDB_Manual.Rmd