Package 'HuBMAPR'

Title: Interface to 'HuBMAP'
Description: 'HuBMAP' provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `files_globus_url()`.
Authors: Christine Hou [aut, cre] , Martin Morgan [aut] , Federico Marini [aut]
Maintainer: Christine Hou <[email protected]>
License: Artistic-2.0
Version: 1.1.0
Built: 2024-10-30 07:29:24 UTC
Source: https://github.com/bioc/HuBMAPR

Help Index

HuBMAP File Querying

Description

bulk_data_transfer() takes a unique dataset or publication UUID to be used to query the HuBMAP API for information about available files.

Usage

bulk_data_transfer(uuid)

Arguments

uuid

character(1) corresponding to the HuBMAP Dataset UUID string. This is expected to be a 32-digit hex number. One unique Dataset UUID corresponds to one specific URL on Globus. Files corresponding to unique Dataset UUID are saved on Globus HuBMAP Public Collection webpage.

Details

Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis

Value

bulk_data_transfer() display information about how to bulk download all files related to the dataset or publication.

Examples

# Globus available
uuid_globus <- "2d3dbd5e5a3d9d5cfc7a46f06815a4eb"
uuid_sra_dbGaP <- "5ba6a5b81e95c93c26a33980f6e957d7"
uuid_not_available <- "0eb5e457b4855ce28531bc97147196b6"

# bulk_data_transfer(*_globus)

Collection Information Summaries from Collection UUID

Description

collection_information() queries the HuBMAP collection for title, description, DOI, URL, creation date, and last modified time date.

print.collection_information() organizes the returned tibble from collection_information() in a more legible format.

Usage

collection_information(uuid)

## S3 method for class 'collection_information'
print(x, ...)

Arguments

uuid

character(1) corresponding to the HuBMAP Collection UUID string. This is expected to be a 32-digit hex number.
x

an object of class collection_information, the result of a call to collection_information().
...

additional arguments, required to conform with the print generic but not used.

Value

collection_information() returns a tibble, and columns containing information about the collection. The tibble is of class collection_information and is printed in character.

print.collection_information() is invoked automatically when the result of collection_information() is displayed for it's side effect of displaying the object.

Examples

uuid <- "90399057f6ff0ff18d4c46a378f0b069"
collection_information(uuid)

HuBMAP Collections

Description

collections() returns details about available collections, 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().

collection_contacts() takes a unique collection_id and returns contacts information of one specified collection as a tibble

collection_data() takes a unique collection_id and returns related datasets of one specified collection as a tibble

collection_contributors() takes a unique collection_id and returns contributors information of one specified collection as a tibble

Usage

collections()

collections_default_columns(as = c("tibble", "character"))

collection_contacts(uuid)

collection_data(uuid)

collection_contributors(uuid)

Arguments

as

character(1) return format. One of "tibble" (default), or "character".
uuid

character(1) corresponding to the HuBMAP Collection UUID string. This is expected to be a 32-digit hex number.

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

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.

Examples

collections()
collections_default_columns()

uuid <- "381f65e58d5e2c1d16a9cef2cc203aab"
collection_contacts(uuid)
uuid <- "381f65e58d5e2c1d16a9cef2cc203aab"
collection_data(uuid)
uuid <- "590b0485a196956284b8f3344276bc50"
collection_contributors(uuid)

HuBMAP Datasets

Description

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)

Arguments

as

character(1) return format. One of "tibble" (default), or "character".
uuid

character(1) corresponding to the HuBMAP Donor UUID string. This is expected to be a 32-digit hex number.

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

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.

Examples

datasets()
datasets_default_columns()

uuid <- "7754aa5ebde628b5e92705e33e74a4ef"
dataset_detail(uuid)
# no derived dataset
uuid <- "3acdb3ed962b2087fbe325514b098101"
dataset_derived(uuid)

# with derived dataset
uuid <- "2c77b1cdf33dbed3dbfb74e4b578300e"
dataset_derived(uuid)
uuid <- "564167adbbb2fdd64c24e7ea409c23f1"
dataset_metadata(uuid)

uuid <- "564167adbbb2fdd64c24e7ea409c23f1"
dataset_contributors(uuid)

HuBMAP Donors

Description

donors() returns details about available samples, 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().

donor_detail() takes a unique donor_id and returns details about one specified sample as a tibble

donor_derived() takes a unique donor_id and returns the derived dataset or/and sample details.

donor_metadata() takes a unique donor_id and returns the metadata of the donor.

Usage

donors()

donors_default_columns(as = c("tibble", "character"))

donor_detail(uuid)

donor_derived(uuid, entity_type = c("Dataset", "Sample"))

donor_metadata(uuid)

Arguments

as

character(1) return format. One of "tibble" (default), or "character".
uuid

character(1) corresponding to the HuBMAP Donor UUID string. This is expected to be a 32-digit hex number.
entity_type

character(1) selected derived entity type. One of "Sample" or "Dataset" (default).

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

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.

Examples

donors()
donors_default_columns()

uuid <- "1dcde05aea3509b2cf89a41ceb3d700f"
donor_detail(uuid)
uuid <- "1dcde05aea3509b2cf89a41ceb3d700f"
donor_derived(uuid, "Sample")

uuid <- "d37df2cad4e80dc368763caefccf7140"
donor_metadata(uuid)

HuBMAP Organs

Description

organ retrieves available organ categories and abbreviations

Usage

organ()

Value

organ returns the tibble with all available organs' abbreviations and corresponding full name.

Examples

organs <- organ()
organs |>
    dplyr::select("name") |>
    dplyr::distinct()

Publication Information Summaries from Publication UUID

Description

publication_information() queries the HuBMAP publication for title, abstract, manuscript,corresponding authors, dataset types, and organ.

publication_information() organizes the returned tibble from publication_information() in a more legible format.

Usage

publication_information(uuid)

## S3 method for class 'publication_information'
print(x, ...)

Arguments

uuid

character(1) corresponding to the HuBMAP Publication UUID string. This is expected to be a 32-digit hex number.
x

an object of class publication_information, the result of a call to publication_information().
...

additional arguments, required to conform with the print generic but not used.

Value

publication_information() returns a tibble, and columns containing information about the publication. The tibble is of class publication_information and is printed in character.

print.publication_information() is invoked automatically when the result of publication_information() is displayed for it's side effect of displaying the object.

Examples

uuid <- "e8338966c69e759157d6c6ad24847989"
publication_information(uuid)

HuBMAP Samples

Description

publications() returns details about available samples, ordered by last modified dates. publication_status == TRUE: peer reviewed publication; publication_status == FALSE: pre-print publication.

⁠*_columns()⁠ returns a tibble or named character vector describing the content of the tibble returned by samples(), datasets(), donors(), collections(), or publications().

publication_data() takes a unique publication_id and returns details about one specified publication.

publication_authors() takes a unique publication_id and returns authors information of one specified collection as a tibble

Usage

publications()

publications_default_columns(as = c("tibble", "character"))

publication_data(uuid, entity_type = c("Dataset", "Sample", "Donor"))

publication_authors(uuid)

Arguments

as

character(1) return format. One of "tibble" (default), or "character".
uuid

character(1) corresponding to the HuBMAP Publication UUID string. This is expected to be a 32-digit hex number.
entity_type

character(1) selected derived entity type. One of "Sample", "Donor" or "Dataset" (default).

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

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.

Examples

publications()
publications_default_columns()

uuid <- "3c7273660cdf9ab91a7901533b2cd9a5"
publication_data(uuid)

uuid <- "3c7273660cdf9ab91a7901533b2cd9a5"
publication_authors(uuid)

HuBMAP Samples

Description

samples() returns details about available samples, ordered by last modified dates. There are multiple tissue sample types displayed in sample_category column which are block, organ, suspension, and section.

⁠*_columns()⁠ returns a tibble or named character vector describing the content of the tibble returned by samples(), datasets(), donors(), collections(), or publications().

sample_detail() takes a unique sample_id and returns details about one specified sample as a tibble

sample_derived() takes a unique sample_id and returns the derived dataset or/and sample details.

sample_metadata() takes a unique donor_id and returns the metadata of the sample.

Usage

samples()

samples_default_columns(as = c("tibble", "character"))

sample_detail(uuid)

sample_derived(uuid, entity_type = c("Dataset", "Sample"))

sample_metadata(uuid)

Arguments

as

character(1) return format. One of "tibble" (default), or "character".
uuid

character(1) corresponding to the HuBMAP Donor UUID string. This is expected to be a 32-digit hex number.
entity_type

character(1) selected derived entity type. One of "Sample" or "Dataset" (default).

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

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.

Examples

samples()
samples_default_columns()

uuid <- "d3525d35f6d5ee3dc3186613b0ab1762"
sample_detail(uuid)
uuid <- "3e7dc14313262af577f686dcb09f5119"
sample_derived(uuid, "Sample")
uuid <- "8d7ce3aab7013e416263d23b0c048900"
sample_metadata(uuid)

HuBMAP Provenance

Description

HuBMAP Provenance

Usage

uuid_provenance(uuid)

Arguments

uuid

character(1) corresponding to the HuBMAP Dataset or Sample UUID string. This is expected to be a 32-digit hex number.

Details

Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis

Value

uuid_provenance() takes a Dataset or Sample UUID, and returns the provenance details as a list of characters, from the most recent ancestor to the furthest ancestor. The entity type of ancestors include Dataset, Sample, and Donor. Note that there is no ancestor for Donor entity such that the returned result will be an empty list.

Examples

uuid <- "acf816bed56dd6ba55da82960d937ec4"
uuid_provenance(uuid)