Package: BgeeDB 2.33.0

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_2.33.0.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'))

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-2.31.2(bioc 3.20)BgeeDB-2.30.2(bioc 3.19)

software dataimport sequencing geneexpression microarray go genesetenrichment bioinformatics enrichment-analysis rna-seq scrna-seq single-cell

7.81 score 14 stars 1 packages 18 scripts 401 downloads 14 exports 91 dependencies

Last updated 23 days agofrom:13c7c42cc4. Checks:OK: 2 ERROR: 4 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	ERROR	Oct 30 2024
R-4.5-linux	ERROR	Oct 30 2024
R-4.4-win	ERROR	Oct 30 2024
R-4.4-mac	OK	Oct 30 2024
R-4.3-win	ERROR	Oct 30 2024
R-4.3-mac	WARNING	Oct 30 2024

Exports:Bgee deleteLocalData deleteOldData formatData getAnnotation getCellProcessedData getData getIntegratedCalls getSampleProcessedData listBgeeRelease listBgeeSpecies loadTopAnatData makeTable topAnat

Dependencies:abind anndata AnnotationDbi askpass assertthat basilisk basilisk.utils Biobase BiocGenerics Biostrings bit bit64 bitops blob bread cachem cli cpp11 crayon curl data.table DBI DelayedArray digest dir.expiry dplyr fansi fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue GO.db graph HDF5Array here httr IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp RcppTOML RCurl reticulate rhdf5 rhdf5filters Rhdf5lib rlang rprojroot RSQLite S4Arrays S4Vectors SingleCellExperiment SparseArray SparseM stringi stringr SummarizedExperiment sys tibble tidyr tidyselect topGO UCSC.utils utf8 vctrs withr XVector zellkonverter zlibbioc

BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests

Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic Bastian

Rendered fromBgeeDB_Manual.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-01
Started: 2016-03-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bgee Reference Class	Bgee Bgee-class
Delete local data for the species of the reference class Bgee object	deleteLocalData
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 processed expression values at cell level for single cell data in Bgee.	getCellProcessedData
Deprecated : Retrieve Bgee RNA-seq or Affymetrix data.	getData
Retrieve Bgee calls from one species.	getIntegratedCalls
Retrieve Bgee processed expression values for bulk RNA-seq, full length single-cell RNA-seq, droplet based single-cell RNA-seq or Affymetrix data.	getSampleProcessedData
List Bgee releases available to use with BgeeDB package	listBgeeRelease
List species in the Bgee database and the available data types for each of them	listBgeeSpecies
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 package	topAnat