rba_jaspar_species {rbioapi}

List available species in JASPAR

Description

JASPAR organizes matrix profiles from multiple species in six taxonomic groups. Use this function to retrieve a list of available species in a JASPAR database release.

Usage

rba_jaspar_species(release = 2024, search = NULL, order = NULL, ...)

Arguments

release

Numeric: (default = 2024) Which JASPAR database release to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.

search

Character: A search term.

order

Character: A character string or a vector of character strings of field names that will be used to order the results.
Providing multiple field names is supported. You can also use prefix "-" before a field name to indicate reverse ordering.

...

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

Value

A data frame with information of available species.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/species/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_species(release = 2024)