Get PANTHER database Information
Using this function you can retrieve a list of available organisms, annotation datasets, families, and pathways which are supported in PANTHER.
rba_panther_info(what, organism_chr_loc = FALSE, families_page = 1, ...)
what |
what information to retrieve? should be one of:
|
organism_chr_loc |
(Logical) (only when 'what = "organisms"') If TRUE, only organisms with chromosome location will be returned. If FALSE (default) every organisms will be returned. |
families_page |
(Numeric) (only when 'what = "families"') Family information is very long, so results are paginated. Use this argument to define the page to retrieve. |
... |
rbioapi option(s). Refer to |
For families, a list and otherwise a data frame with pertinent information.
"GET http://www.pantherdb.org/services/oai/pantherdb/supportedgenomes"
"GET http://www.pantherdb.org/services/oai/pantherdb/supportedannotdatasets"
"GET http://www.pantherdb.org/services/oai/pantherdb/supportedpantherfamilies"
"GET http://www.pantherdb.org/services/oai/pantherdb/supportedpantherpathways"
Mi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2019). PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic acids research, 47(D1), D419-D426.
Mi, H., Muruganujan, A., Huang, X., Ebert, D., Mills, C., Guo, X., & Thomas, P. D. (2019). Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v. 14.0). Nature protocols, 14(3), 703-721.
Other "PANTHER":
rba_panther_enrich(),
rba_panther_family(),
rba_panther_homolog(),
rba_panther_mapping(),
rba_panther_ortholog(),
rba_panther_tree_grafter()
rba_panther_info(what = "organisms") rba_panther_info(what = "families", families_page = 4)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.