DescriptionPathway analysis is a common task in genomics research and there are many available R-based software tools. Depending on the tool, it may be necessary to import the pathways, translate genes to the appropriate species, convert between symbols and IDs, and format the resulting object. The msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used with the Gene Set Enrichment Analysis (GSEA) software: in an R-friendly tidy/long format with one gene per row for multiple frequently studied model organisms, such as mouse, rat, pig, zebrafish, fly, and yeast, in addition to the original human genes as gene symbols as well as NCBI Entrez and Ensembl IDs that can be installed and loaded as a package without requiring additional external files Please be aware that the homologs were computationally predicted for distinct genes. The full pathways may not be well conserved across species.
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