| ArrayExpressHTS | ExpressionSet for RNA-Seq experiment submitted in ArrayExpress and ENA |
| ArrayExpressHTSFastQ | ExpressionSet for RNA-Seq raw data files |
| getDefaultFilteringOptions | Functions to work with ArrayExpressHTS processing options |
| getDefaultProcessingOptions | Functions to work with ArrayExpressHTS processing options |
| getDefaultRCloudOptions | Functions to work with ArrayExpressHTS processing options |
| getPipelineOption | Functions to work with package level options |
| getPipelineOptions | Functions to work with package level options |
| isRCloud | Check the code is running on R-Cloud |
| prepareAnnotation | Prepare annotation data for the RNA-Seq Pipeline |
| prepareReference | Prepare reference data for the RNA-Seq Pipeline |
| setPipelineOptions | Functions to work with package level options |