Overview | Installation | Basic User Guide | Implementation Notes | Load Necessary Packages | Data Discovery | Data Wrangling Examples | Metadata | Derived Data | Provenance Data | Related Data | Additional Information | File Transfer | Files are publicly accessible | Alternative data transfer method using rglobus package | Files are restricted | Files are unavailable | R session information
Package: HuBMAPR 1.6.2
Christine Hou
HuBMAPR: Interface to 'HuBMAP'
'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 `bulk_data_transfer()`.
Authors:
HuBMAPR_1.6.2.tar.gz
HuBMAPR_1.6.2.zip(r-4.7)HuBMAPR_1.6.2.zip(r-4.6)HuBMAPR_1.6.2.zip(r-4.5)
HuBMAPR_1.6.2.tgz(r-4.6-any)HuBMAPR_1.6.2.tgz(r-4.5-any)
HuBMAPR_1.6.2.tar.gz(r-4.7-any)HuBMAPR_1.6.2.tar.gz(r-4.6-any)
HuBMAPR_1.6.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HuBMAPR/json (API)
| # Install 'HuBMAPR' in R: |
| install.packages('HuBMAPR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/christinehou11/hubmapr/issues
Pkgdown/docs site:https://christinehou11.github.io
On BioConductor:HuBMAPR-1.7.1(bioc 3.24)HuBMAPR-1.6.1(bioc 3.23)
softwaresinglecelldataimportthirdpartyclientspatialinfrastructurebioconductor-packageclienthubmaprstudio
Last updated from:e770872f08 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 169 | ||
| linux-devel-x86_64 | OK | 261 | ||
| source / vignettes | OK | 207 | ||
| linux-release-x86_64 | OK | 231 | ||
| macos-release-arm64 | OK | 135 | ||
| macos-oldrel-arm64 | OK | 141 | ||
| windows-devel | OK | 151 | ||
| windows-release | OK | 139 | ||
| windows-oldrel | OK | 155 | ||
| wasm-release | OK | 104 |
Exports:bulk_data_transfercollection_contactscollection_contributorscollection_datacollection_detailcollection_informationcollectionscollections_default_columnsdataset_contributorsdataset_deriveddataset_detaildataset_metadatadatasetsdatasets_default_columnsdonor_deriveddonor_detaildonor_metadatadonorsdonors_default_columnsorganpublication_authorspublication_datapublication_informationpublicationspublications_default_columnssample_derivedsample_detailsample_metadatasamplessamples_default_columnsuuid_provenance
Dependencies:askpassclicpp11curldplyrgenericsgluehttr2lifecyclemagrittropensslpillarpkgconfigpurrrR6rappdirsrjsonconsrlangstringistringrsystibbletidyrtidyselectutf8vctrswhiskerwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| HuBMAP File Querying | bulk_data_transfer |
| Collection Information Summaries from Collection UUID | collection_information print.collection_information |
| HuBMAP Collections | collections collections_default_columns collection_contacts collection_contributors collection_data collection_detail |
| HuBMAP Datasets | datasets datasets_default_columns dataset_contributors dataset_derived dataset_detail dataset_metadata |
| HuBMAP Donors | donors donors_default_columns donor_derived donor_detail donor_metadata |
| HuBMAP Organs | organ |
| Publication Information Summaries from Publication UUID | print.publication_information publication_information |
| HuBMAP Samples | publications publications_default_columns publication_authors publication_data |
| HuBMAP Samples | samples samples_default_columns sample_derived sample_detail sample_metadata |
| HuBMAP Provenance | uuid_provenance |
