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 | Draw the graph of the significant conditions | Test the propagated calls without decorrelation | Store expression data localy

How present/absent calls are generated | Bgee database | Reference intergenic regions | Threshold of present/absent | Installation | How to use the BgeeCall package | Load the package | Quick start | Generate present/absent calls for more than one RNA-Seq library | Parallized generation of present/absent calls on a cluster | Reference intergenic sequences | Releases of reference intergenic sequences | Core reference intergenic from Bgee | Community reference intergenic | Your own reference intergenic | Generate present/absent calls at transcript level (beta version) | Tune how to use kallisto | Download or reuse your own kallisto | Edit kallisto quant attributes | Choose between two kmer size | Generate calls for a subset of RNA-Seq runs | Modify present/absent threshold | Default pValue approach | Intergenic threshold approach | qValue threshold approach | Run BgeeCall in quiet mode | Do not rerun parts of the pipeline | Ignore transcript version | Generate calls with a simple arborescence of directories | Change directory where calls are saved | Modify slurm options | Number of jobs | Do not submit the jobs | Modify slurm options | Add modules to your environment | Modify BgeeCall objects | Merging multiple libraries | Arguments and user file to perform the merging