BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests
Installation | How to use BgeeDB package | Load the package | Running example: downloading and formatting processed RNA-seq data | List available species in Bgee | Create a new Bgee object | Retrieve the annotation of zebrafish RNA-seq datasets | Download the processed zebrafish bulk RNA-seq data | Format the sample level bulk RNA-seq data | Download cell level single-cell RNA-seq data | Running example: TopAnat gene expression enrichment analysis | Download the data allowing to perform TopAnat analysis | Prepare a topAnatData object allowing to perform TopAnat analysis with topGO | Launch the enrichment test | Format the table of results after an enrichment test for anatomical terms | Store expression data localy
Rendered fromBgeeDB_Manual.Rmdusingknitr::rmarkdown