Experiment

class pyrefinebio.Experiment(id=None, title=None, description=None, technology=None, annotations=None, samples=None, protocol_description=None, accession_code=None, alternate_accession_code=None, source_database=None, source_url=None, has_publication=None, publication_title=None, publication_doi=None, publication_authors=None, pubmed_id=None, source_first_published=None, source_last_modified=None, submitter_institution=None, platform_names=None, platform_accession_codes=None, last_modified=None, created_at=None, organism_names=None, downloadable_organism_names=None, sample_metadata_fields=None, sample_metadata=None, num_total_samples=None, num_processed_samples=None, num_downloadable_samples=None)

Retrieve an Experiment based on id

>>> import pyrefinebio
>>> accession_code = 1
>>> experiment = pyrefinebio.Experiment.get(accession_code)

Search for Experiments based on filters

>>> import pyrefinebio
>>> experiments = pyrefinebio.Experiment.search(is_compendia=True, is_public=True)
classmethod get(accession_code)

Retrieve an Experiment based on accession code

Returns:

Experiment

Parameters:

code (accession) – the accession code for the Experiment you want to get

classmethod search(**kwargs)

Search for Experiments based on various filters

Returns:

list of Experiment

Keyword Arguments:

  • id (int) – filter based on the id of the Experiment

  • technology (str) – filter based on the technology used for the Experiment (microarray, rna-seq, etc) this filter can have multiple values.

  • has_publication (bool) – filter based on if the Experiment has associated publications

  • accession_code (str) – filter based on the Experiment’s accession code this filter can have multiple values

  • alternate_accession_code (str) – filter based on the Experiment’s alternate accession codes

  • platform (str) – filter based on platform, this filter can have multiple values

  • organism (str) – filter based on Organism, this filter can have multiple values

  • downloadable_organism (str) – filter based on Organisms that have downloadable files, this filter can have multiple values

  • num_processed_samples (number) – filter based on the Experiment’s number of processed samples

  • num_downloadable_samples (int) – filter based on the Experiment’s number of downloadable samples

  • sample_keywords (str) – filter based on keywords associated with the Experiment’s Samples

  • ordering (str) – which field from to use when ordering the results

  • search (str) – specify a keyword which will be applied to the Experiment’s title, publication_authors, sample_keywords, publication_title, submitter_institution, description, accession_code, alternate_accession_code, publication_doi, pubmed_id, sample_metadata_fields, and platform_names

  • limit (int) – number of results to return per page

  • offset (int) – the initial index from which to return the results