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Retrieve a List of available libraries from Enrichr

Source: R/enrichr.R
rba_enrichr_libs.Rd

This function retrieves a list of libraries available in Enrichr along with their associated statistics. Each library represents a collection of gene sets that can be used for enrichment analysis.

Usage

rba_enrichr_libs(organism = "human", store_in_options = TRUE, ...)

Arguments

organism

(default = "human") Which model organism version of Enrichr to use? Available options are: "human", (H. sapiens & M. musculus), "fly" (D. melanogaster), "yeast" (S. cerevisiae), "worm" (C. elegans) and "fish" (D. rerio).

store_in_options

logical: (default = TRUE) Should a list of available Enrichr libraries be saved as a global option?

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A data frame with the names of available library in Enrichr and their statistics.

Details

By default, this function will save the library names as a global option ("rba_enrichr_libs") for other Enrichr functions that internally require the names of Enrichr libraries. You should call this function once per R session with the argument 'store_in_options = TRUE' before using rba_enrichr_enrich or rba_enrichr. However, if you do not explicitly call it, rbioapi will automatically execute this function in the background the when it is needed.

Please note that rba_enrichr provides a one-step and more convenient way to automatically handle this and other required function calls needed to perform gene set enrichment analysis with Enrichr.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/datasetStatistics"

References

  • Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

  • Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

  • Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

  • Enrichr API Documentation

  • Citations note on Enrichr website

See also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_view_list()

Examples

# \donttest{
rba_enrichr_libs()
# }