get_experiment_catalog: Complete list of all experiments in refine.bio

In seandavi/RefineBio: The bridge between refine.bio and Bioconductor

Complete list of all experiments in refine.bio

Description

Refine.bio experiments are collections of samples that were processed together. In practices, refine.bio experiments are usually a GEO series or an SRA study. This function returns a list of all experiments in refine.bio as a tibble.

Usage

get_experiment_catalog(.pages = 1e+05)

Arguments

.pages

integer(1) The number of pages to retrieve (with default=Inf). Generally, you'll want to ignore this; it's only useful for testing.

Value

tibble A tibble of all experiments in refine.bio.

The tibble contains the following columns:

• id: The ID of the experiment

• title: The title of the experiment

• publication_title: The title of the publication associated with the experiment

• description: A description of the experiment

• accession_code: The accession code of the experiment

• alternate_accession_code: An alternate accession code for the experiment

• technology: The technology used to generate the data in the experiment

• submitter_institution: The institution that submitted the experiment

• has_publication: Whether the experiment has a publication associated with it

• publication_doi: The DOI of the publication associated with the experiment

• publication_authors: The authors of the publication associated with the experiment

• pubmed_id: The PubMed ID of the publication associated with the experiment

• source_first_published: The date the experiment was first published

• num_total_samples: The total number of samples in the experiment

• num_processed_samples: The number of samples in the experiment that have been processed

• num_downloadable_samples: The number of samples in the experiment that are downloadable

• platform_names: The names of the platforms used in the experiment

• organism_names: The names of the organisms in the experiment

• sample_metadata_fields: The types of metadata available for the samples in the experiment

• samples: a data.frame of sample metadata

Author(s)

• Sean Davis [e-mail]

• Alex Ho [e-mail]

Examples

# this takes about 1-2 minutes to complete
# for the entire experiment listing
# depending on your internet connection
# You only need to do this once (or when you want
#   to update the results)

# get the first 2 pages of experiments for
# testing and demonstration purposes
experiments <- experiment_listing(.pages = 2)

# get all experiments
# experiments <- get_experiment_catalog()

head(experiments)
dim(experiments)
colnames(experiments)

seandavi/RefineBio documentation built on June 1, 2025, 4:10 p.m.