Get PANTHER Families and Sub-Families
Using this function, you can retrieve Orthologs, MSA or Tree topology information of a given PANTHER family.
rba_panther_family(id, what, target_organisms = NA, ...)
id |
Panther family id. |
what |
What to retrieve? One of:
|
target_organisms |
(numeric) NCBI taxon ID(s) to filter the results.
run |
... |
rbioapi option(s). Refer to |
For trees a list and otherwise a data frame with the requested family's information.
"GET http://www.pantherdb.org/services/oai/pantherdb/familyortholog"
"GET http://www.pantherdb.org/services/oai/pantherdb/familymsa"
"GET http://www.pantherdb.org/services/oai/pantherdb/treeinfo"
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_homolog(),
rba_panther_info(),
rba_panther_mapping(),
rba_panther_ortholog(),
rba_panther_tree_grafter()
rba_panther_family("PTHR10000", what = "ortholog")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.