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: 3,487 × 14
#> uuid hubmap_id dataset_type dataset_type_additio…¹ organ analyte_class
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 fa41085335… HBM995.V… RNAseq "" Uter… RNA
#> 2 8f52ffc9dd… HBM474.Q… RNAseq "" Uter… RNA
#> 3 0189bfe5ec… HBM272.X… Histology "" Uter… nucleic acid…
#> 4 d3adb9f148… HBM796.J… RNAseq "" Fall… RNA
#> 5 416b162c70… HBM866.D… RNAseq "" Uter… RNA
#> 6 f70aa16de6… HBM722.Z… Histology "" Ovar… nucleic acid…
#> 7 3e56e5a7c2… HBM674.K… Histology "" Uter… nucleic acid…
#> 8 c0846c02ff… HBM634.W… Histology "" Uter… nucleic acid…
#> 9 5531f0fe13… HBM528.M… RNAseq "" Uter… RNA
#> 10 f09be53548… HBM586.G… Histology "" Uter… nucleic acid…
#> # ℹ 3,477 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)
#> # A tibble: 29 × 2
#> Key Value
#> <chr> <chr>
#> 1 acquisition_instrument_model BZ-X710
#> 2 acquisition_instrument_vendor Keyence
#> 3 analyte_class Polysaccharide
#> 4 contributors_path extras/contributors.tsv
#> 5 data_path .
#> 6 dataset_type Histology
#> 7 is_batch_staining_done No
#> 8 is_image_preprocessing_required No
#> 9 is_staining_automated No
#> 10 is_targeted No
#> # ℹ 19 more rows
uuid <- "564167adbbb2fdd64c24e7ea409c23f1"
dataset_contributors(uuid)
#> # A tibble: 3 × 5
#> display_name affiliation email orcid is_principal_investi…¹
#> <chr> <chr> <chr> <chr> <chr>
#> 1 John Hickey Stanford john.hickey@duke.edu 0000… No
#> 2 Chiara Caraccio Stanford caraccio@stanford.edu 0000… No
#> 3 Garry Nolan Stanford gnolan@stanford.edu 0000… Yes
#> # ℹ abbreviated name: ¹is_principal_investigator