Skip to contents

Prior to perform enrichment, Enrichr requires you to upload your gene-list and retrieve a 'user list ID'.

Usage

rba_enrichr_add_list(gene_list, description = NULL, organism = "human", ...)

Arguments

gene_list

A vector with Entrez gene symbols.

description

(optional) A name or description to be associated with your uploaded gene-set to Enrichr servers.

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).

...

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

Value

A list with two unique IDs for your uploaded gene sets.

Details

Note that using rba_enrichr is a more convenient way to automatically perform this and other required function calls to enrich your input gene-set.

Corresponding API Resources

"POST https://maayanlab.cloud/Enrichr/addList"

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: https://doi.org/10.1002/cpz1.90

  • Enrichr API Documentation

  • Citations note on Enrichr website

Examples

# \donttest{
rba_enrichr_add_list(gene_list = c("TP53", "TNF", "EGFR"),
     description = "tumoral genes")
# }