datasets returns the details available datasets, ordered by
last modified dates
*_columns() returns a tibble or named
character vector describing the content of the tibble returned
by samples(), datasets(), donors(), collections(),
or publications().
dataset_detail() takes a unique dataset_id and
returns details about one specified dataset as a tibble
dataset_derived() takes a unique sample_id and
returns the derived (support) dataset details. Support datasets normally
belong to Image Pyramid, with image files available to download via
Globus Collection. See details to download in files_globus_url().
dataset_metadata() takes a unique dataset_id and
returns the metadata of the dataset.
dataset_contributors() takes a unique dataset_id and
returns the contributors of the dataset. For questions for this
dataset, reach out to the individuals listed as contacts, either via
the email address listed in the table or contact information provided
on their ORCID profile page.
Usage
datasets()
datasets_default_columns(as = c("tibble", "character"))
dataset_detail(uuid)
dataset_derived(uuid)
dataset_metadata(uuid)
dataset_contributors(uuid)Value
*_columns() returns a named list name
containing the column name used in the tibble returned by
samples(), datasets(), donors(),
collections(), or publications().
When as = "tibble",the return value is a tibble
with paths as elements and abbreviations as names.
Details
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Examples
datasets()
#> # A tibble: 3,691 × 14
#> uuid hubmap_id dataset_type dataset_type_additio…¹ organ analyte_class
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 997e75072d… HBM236.G… 10X Multiome "" Ovar… ""
#> 2 7036a70229… HBM399.V… Histology "" Lung… "Nucleic aci…
#> 3 c15f813973… HBM399.S… Histology "" Lung… ""
#> 4 ca302925f0… HBM234.V… Histology "" Larg… "Nucleic aci…
#> 5 aed6880fb3… HBM958.B… Histology "" Larg… "Nucleic aci…
#> 6 b0c21c4002… HBM875.H… Histology "" Larg… "Nucleic aci…
#> 7 bfda5e0865… HBM793.K… Histology "" Larg… "Nucleic aci…
#> 8 baf976734d… HBM468.M… Histology "" Smal… "Nucleic aci…
#> 9 57b475b8ad… HBM579.L… Histology "" Smal… "Nucleic aci…
#> 10 856aa4e05b… HBM433.H… Histology "" Smal… "Nucleic aci…
#> # ℹ 3,681 more rows
#> # ℹ abbreviated name: ¹dataset_type_additional_information
#> # ℹ 8 more variables: sample_category <chr>, status <chr>,
#> # dataset_processing_category <chr>, pipeline <chr>, registered_by <chr>,
#> # donor_hubmap_id <chr>, group_name <chr>, last_modified_timestamp <chr>
datasets_default_columns()
#> # A tibble: 14 × 1
#> columns
#> <chr>
#> 1 uuid
#> 2 hubmap_id
#> 3 group_name
#> 4 dataset_type_additional_information
#> 5 dataset_type
#> 6 organ
#> 7 analyte_class
#> 8 dataset_processing_category
#> 9 sample_category
#> 10 registered_by
#> 11 status
#> 12 pipeline
#> 13 last_modified_timestamp
#> 14 donor_hubmap_id
uuid <- "7754aa5ebde628b5e92705e33e74a4ef"
dataset_detail(uuid)
#> # A tibble: 1 × 31
#> ancestor_ids ancestors contains_human_genetic_sequen…¹ created_by_user_disp…²
#> <list> <list> <lgl> <chr>
#> 1 <chr [4]> <list [4]> FALSE HuBMAP Process
#> # ℹ abbreviated names: ¹contains_human_genetic_sequences,
#> # ²created_by_user_displayname
#> # ℹ 27 more variables: created_by_user_email <chr>, created_timestamp <dbl>,
#> # creation_action <chr>, data_access_level <chr>, data_types <list>,
#> # dataset_info <chr>, dataset_type <chr>, descendant_ids <list>,
#> # descendants <list>, display_subtype <chr>, donor <list>, entity_type <chr>,
#> # files <list>, group_name <chr>, group_uuid <chr>, hubmap_id <chr>, …
# no derived dataset
uuid <- "3acdb3ed962b2087fbe325514b098101"
dataset_derived(uuid)
#> NULL
# with derived dataset
uuid <- "2c77b1cdf33dbed3dbfb74e4b578300e"
dataset_derived(uuid)
#> # A tibble: 1 × 6
#> uuid hubmap_id data_types dataset_type status last_modified_timest…¹
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 9e7b040f23124… "" "" RNAseq [Sal… "" NA
#> # ℹ abbreviated name: ¹last_modified_timestamp
uuid <- "564167adbbb2fdd64c24e7ea409c23f1"
dataset_metadata(uuid)
#> New names:
#> • `` -> `...1`
#> # A tibble: 28 × 2
#> Key Value
#> <chr> <chr>
#> 1 acquisition_instrument_model "BZ-X710"
#> 2 acquisition_instrument_vendor "Keyence"
#> 3 analyte_class "Nucleic acid + protein"
#> 4 contributors_path "extras/contributors.tsv"
#> 5 data_path "."
#> 6 dataset_type "Histology"
#> 7 intended_tile_overlap_percentage ""
#> 8 is_batch_staining_done "No"
#> 9 is_image_preprocessing_required "No"
#> 10 is_staining_automated "No"
#> # ℹ 18 more rows
uuid <- "564167adbbb2fdd64c24e7ea409c23f1"
dataset_contributors(uuid)
#> # A tibble: 3 × 11
#> affiliation display_name email first_name is_contact is_operator
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Stanford John Hickey john.hickey@duk… John Yes Yes
#> 2 Stanford Chiara Caraccio caraccio@stanfo… Chiara Yes Yes
#> 3 Stanford Garry Nolan gnolan@stanford… Garry Yes No
#> # ℹ 5 more variables: is_principal_investigator <chr>, last_name <chr>,
#> # metadata_schema_id <chr>, middle_name_or_initial <chr>, orcid <chr>