mosdef: a collection of MOSt frequently used and useful Differential Expression Functions

Author(s): Leon Dammer,Federico Marini

Affiliation(s): Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany



The mosdef R package offers a comprehensive toolkit for simplifying and streamlining some common operations in the workflow of differential expression analysis. By providing a unified interface for executing various enrichment analysis tools, mosdef allows researchers to effortlessly run such functions (e.g. from topGO, goseq, or clusterProfiler) , directly using the standard containers for such workflows. mosdef also includes functions to create standard graphical representations such as volcano and MA plots, making them easy to customize and extend (e.g. highlighting specific Gene Ontology signatures). Moreover, mosdef facilitates and beautifies the creation of RMarkdown reports with functionality to seamlessly link output tables to external databases (e.g. PubMed, GeneCards, UniProt, AmiGO, etc.), simplifying the process of contextualizing the ever increasing set of results stemming from many such workflows. Originally intended as a refactoring effort for some of the core functionality provided within pcaExplorer, ideal, and GeneTonic, mosdef will be expanded to provide these facilities also for other widely used DE workflows, such as edgeR and limma. All in all, we think this can become a valuable companion to generate information-rich output, with an API that directly links to the commonly adopted data containers in the Bioconductor ecosystem. This will assist both experienced and more novice users with any background to perform the many steps around the differential expression workflow and communicate their findings efficiently. mosdef is available on Bioconductor since its latest release at https://www.bioconductor.org/packages/mosdef.