Without requiring active engagement on its website (https://toppgene.cchmc.org/), the scToppR package offers a ToppGene interface from R programs/scripts to fully access/control the database for functional enrichment.
By working with ToppGene, downloading the functional enrichment dataframes, and using the R environment to visualise the outcomes, the library makes functional enrichment analysis and visualisation easier.
Currently, the code and documentation may be found at https://github.com/BioinformaticsMUSC/scToppR.
Reference:
Granger B. et. al. (2024) scToppR: a coding-friendly R interface to ToppGene. Bioinformatics 40 (11) : btae582
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