Introduction | Installation | Usage | Importing the Ontology | Alternative 1: Importing the Ontology from a GMT File | A) mulea GMT File | B) Enrichr GMT File | C) MsigDB GMT File | Alternative 2: Importing the Ontology with the muleaData Package | Filtering the Ontology | Saving the Ontology as a GMT file | Converting a List to an Ontology Object | The Differential Expression Dataset to Analyse | The Unordered Set-Based Overrepresentation Analysis (ORA) | Reading the Target and the Background Sets from Text Files | Performing the OverRepresentation Analysis | Examining the ORA Result | Visualising the ORA Result | Comparing the significant results when applying the eFDR to the Benjamini-Hochberg and the Bonferroni corrections | Gene Set Enrichment Analysis (GSEA) | Reading the Tab Delimited File Containing the Ordered Set | Performing the Gene Set Enrichment Analysis | Examining the GSEA Results | Visualising the GSEA Results | Formatting the Results of a Differential Expression Analysis | Understanding the Differential Expression Results Table | Data Preparation: | Preparing Input Data for the ORA | Target Set | Background Set | Preparing Input Data for the GSEA | Session Info | How to Cite the mulea Package? | References

Download genome assemblies | Download metadata | Parse metadata files

Getting Identifiers | Retrieving Chemical Properties

hoardr introduction | Install | initialize client | set cache path | make the directory if doesn't exist | put a file in the cache | list the files | details | delete by file name