Organism

class pyrefinebio.Organism(name=None, taxonomy_id=None, has_compendia=None, has_quantfile_compendia=None)

Organism.

Retrieve an Organism by name

>>> import pyrefinebio
>>> name = "GORILLA"
>>> organism = pyrefinebio.Organism.get(name)

Retrieve a list of Organisms

>>> import pyrefinebio
>>> organisms = pyrefinebio.Organism.search(has_compendia=True)

classmethod get(name)

Retrieve an Organism based on name

Returns:

Organism

Parameters:

name (str) – the name for the Organism you want to get

classmethod search(**kwargs)

Retrieve a list of Organisms based on filters

Returns:

list of Organism

Keyword Arguments:

• has_compendia (bool) – filter based on if this Organism has a normalized Compendium associated with it

• has_quantfile_compendia (bool) – filter based on if this Organism has an RNA-seq Sample Compendium associated with it