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Complete list of all experiments in refine.bio

Source: R/search.R
experiment_listing.Rd

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

experiment_listing(.pages = Inf)

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

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 <- experiment_listing()

head(experiments)
#> # A tibble: 6 × 21
#>      id title            publication_title description technology accession_code
#>   <int> <chr>            <chr>             <chr>       <chr>      <chr>         
#> 1 52090 Shared and dist… Shared and disti… Neocortex … RNA-SEQ    SRP150473     
#> 2 51049 Transcriptome a… Conserved proper… RNA sequen… RNA-SEQ    SRP118985     
#> 3 47744 In vivo molecul… Broadly neutrali… Dengue vir… RNA-SEQ    SRP152576     
#> 4 67685 Drug-induced ch… The NCI Transcri… To identif… MICROARRAY GSE116436     
#> 5 50699 Single-cell tra… Classes and cont… We  studie… RNA-SEQ    SRP109000     
#> 6 51542 Single cell RNA… Diversity of Int… In order t… RNA-SEQ    SRP124669     
#> # ℹ 15 more variables: alternate_accession_code <chr>,
#> #   submitter_institution <chr>, has_publication <lgl>, publication_doi <chr>,
#> #   publication_authors <list>, sample_metadata_fields <list>,
#> #   platform_names <list>, platform_accession_codes <list>,
#> #   organism_names <list>, downloadable_organism_names <list>, pubmed_id <chr>,
#> #   num_total_samples <int>, num_processed_samples <int>,
#> #   num_downloadable_samples <int>, source_first_published <date>
dim(experiments)
#> [1] 2000   21
colnames(experiments)
#>  [1] "id"                          "title"                      
#>  [3] "publication_title"           "description"                
#>  [5] "technology"                  "accession_code"             
#>  [7] "alternate_accession_code"    "submitter_institution"      
#>  [9] "has_publication"             "publication_doi"            
#> [11] "publication_authors"         "sample_metadata_fields"     
#> [13] "platform_names"              "platform_accession_codes"   
#> [15] "organism_names"              "downloadable_organism_names"
#> [17] "pubmed_id"                   "num_total_samples"          
#> [19] "num_processed_samples"       "num_downloadable_samples"   
#> [21] "source_first_published"