Introduction | What do you get with EMMA? | How does EMMA work? | Installation | Usage example of EMMA: the macrophage dataset | About the data | Getting a list of Differentially Expressed Genes | Performing Functional Enrichment Analysis (FEA) | Entering the EMMA framework | EMMA_run(): Capturing the recorded information | EMMA_show(): Summarizing the recorded information | EMMA_get_record(): Retrieving the recorded information | EMMA_explain(): Summarizing recorded information into text | EMMA with custom/wrapper functions | EMMA_add_custom_metadata(): Adding extra information | EMMA_freeze(): Recording the Analysis Environment | EMMA with iterative workflows | Supported methods and future extensions | Session info | References

Introduction | Why do we need a new class? | Anatomy of DeeDeeExperiment | Creating a DeeDeeExperiment object | Getting started | DeeDeeExperiment on the macrophage dataset | DEA: DESeq2 framework | DEA: limma framework | DEA: edgeR framework | Creating DeeDeeExperiment the DeeDee way | Adding results to a dde object | Adding DEA results | Adding multi-contrast DEA results | Adding FEA results | Linking DE and FE Analysis in a dde object | Adding contextual information | Summary of a dde object | Renaming results in a dde object | Removing results in a dde object | Accessing results stored in a dde object | Downstream operations with DeeDeeExperiment objects | FAQs | Session info | References

Differential State (DS) analysis with muscat & DeeDeeExperiment | DeeDeeExperiment on the Kang dataset | Session info | References

Introduction | Getting started | Create an initial state for gene expression visualization using iSEEinit() | Create an initial state for feature sets exploration using iSEEnrich() | Create an initial state for marker gene exploration using iSEEmarker() | Visualize a preview of the initial configurations with view_initial_tiles() | Visualize network connections between panels with view_initial_network() | Merge different initial configurations with glue_initials() | Related work | Session info