Introduction | The RflomicsMAE and RflomicsSE classes | Methods for RflomicsMAE and RflomicsSE classes | Instantiating a RflomicsMAE object from a MAE object | Overview of the main methods | Executing the workflow : | Define the statistical settings: model and contrasts | Single-omics analysis | Data processing and quality control | Differential analysis: settings and results | Co-expression analysis: settings and results | Annotation enrichment analysis: settings and results | Multi-omics integration analysis | Generating a report from the RflomicsMAE object | Session information

Introduction | Install and run RFLOMICS | Guided tour of the interface | Load Data | Dataset example description | Load Experimental Design | Load Omics data | Set the statistical framework | Single omics data analysis | Data processing and quality check | Completeness check | Transcriptomics data | Differential expression analysis | Coexpression analysis | Annotation and Enrichment analysis using clusterProfiler | Dataset analysis summary | Integration | MOFA | MixOmics | Exploring results from RFLOMICS | Using RFLOMICS without the interface | Load example data | Create a RflomicsMAE object | Session Info

Experimental design file | Omics data file | Transcriptomics (RNAseq counts data) | Proteomics data | Metabolomics data | Annotation of features (optional)