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Gene Set Enrichment and Pathway Analysis

More Information and Resources

This guide is not an exhaustive list of all of the free options for pathway discovery, gene set enrichment, or interaction networks. Users are encouraged to discover pathway or network tools that work best for their own personal preferences, experimental data, and technical expertise.

  • Users who have experience using the R statistical software can find a number of packages available at bioconductor for gene set enrichment or for pathway analysis.
  • Python users can find a Bio.Pathway library and a Bio.KEGG package as part of the biopython package.
  • Many other pathway databases and resources are available. A Google search can discover many more options. Users should pay close attention to the frequency of update of pathway sources.