bgeedb/bgee_r repository overview

Container for BgeeCall and BgeeDB R Bioconductor packages.

BgeeCall: automatic RNA-Seq present/absent gene expression calls generation.

Reference intergenic regions are generated by the Bgee RNA-Seq pipeline. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. BgeeCall now allows to generate present/absent calls for any RNA-Seq library as long as reference intergenic sequences have been generated for the corresponding species. The threshold of present/absent expression is no longer arbitrary defined but is calculated based on expression of all RNA-Seq libraries integrated in Bgee. https://github.com/BgeeDB/BgeeCall⁠

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. https://github.com/BgeeDB/BgeeDB_R⁠

The container contains all libraries to run the Bgee online course https://lnkd.in/gzSbzEA⁠
https://sfonsecacosta.github.io/Bgee/⁠
https://jwollbrett.github.io/BgeeCall_practical/⁠

Run the container with the command

docker run --name bgee_r --rm -it bgeedb/bgee_r:tagname R

You can inspect the container and get packages information (R itself and R libraries, Kallisto, ...), description, license, ... with

docker inspect bgeedb/bgee_r:tagname