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.

rba_jaspar_species(release = 2020, search = NULL, order = NULL, ...)

Arguments

release

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

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 "http://jaspar.genereg.net/api/v1/species/"

References

  • Fornes O, Castro-Mondragon JA, Khan A, et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2019; doi: 10.1093/nar/gkz1001

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

  • Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018; 46:D260–D266, doi: 10.1093/nar/gkx1126

  • JASPAR API Documentation

See also

Examples

# \donttest{
rba_jaspar_species(release = 2020)
# }