Package: GenomicDataCommons 1.31.0
Sean Davis
GenomicDataCommons: NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Authors:
GenomicDataCommons_1.31.0.tar.gz
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GenomicDataCommons.pdf |GenomicDataCommons.html✨
GenomicDataCommons/json (API)
NEWS
| # Install 'GenomicDataCommons' in R: |
| install.packages('GenomicDataCommons', repos = c('https://link-ny.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/genomicdatacommons/issues
On BioConductor:GenomicDataCommons-1.29.7(bioc 3.20)GenomicDataCommons-1.28.2(bioc 3.19)
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
Last updated 23 days agofrom:b90f2c6c22. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | OK | Oct 30 2024 |
| R-4.5-linux | OK | Oct 29 2024 |
| R-4.4-win | OK | Oct 30 2024 |
| R-4.4-mac | OK | Oct 30 2024 |
| R-4.3-win | OK | Oct 30 2024 |
| R-4.3-mac | OK | Oct 30 2024 |
Exports:aggregationsannotationsavailable_expandavailable_fieldsavailable_valuescasescnv_occurrencescnvscountdefault_fieldsendpointsentity_nameexpandfacetfield_descriptionfilesfiltergdc_cachegdc_clientgdc_client_version_validategdc_clinicalgdc_set_cachegdc_tokengdcdatagenesget_facetsget_filtergrep_fieldsid_fieldidsmake_filtermanifestmappingparametersprojectsqueryreadDNAcopyreadHTSeqFileresponseresponse_allresultsresults_allselectslicingssm_occurrencesssmsstatustransfertransfer_helpwrite_manifest
Dependencies:askpassBiocGenericsbitbit64clicliprcpp11crayoncurldplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6rappdirsreadrrlangS4VectorsstringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrxml2XVectorzlibbioc
The GenomicDataCommons Package
Rendered fromoverview.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2024-05-06
Started: 2016-06-20
Questions and answers from over the years
Rendered fromquestions-and-answers.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2024-05-15
Started: 2021-08-09
Working with simple somatic mutations
Rendered fromsomatic_mutations.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2024-05-06
Started: 2020-01-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GenomicDataCommons: A package for interfacing with the NCI GDC | GenomicDataCommons-package GenomicDataCommons |
| aggregations | aggregations aggregations.GDCQuery aggregations.GDCResponse |
| Return valid values for "expand" | available_expand available_expand.character available_expand.GDCQuery |
| S3 Generic to return all GDC fields | available_fields available_fields.character available_fields.GDCQuery |
| Find common values for a GDC field | available_values |
| provide count of records in a 'GDCQuery' | count count.GDCQuery count.GDCResponse |
| S3 Generic to return default GDC fields | default_fields default_fields.character default_fields.GDCQuery |
| Get the entity name from a GDCQuery object | entity_name entity_name.GDCQuery entity_name.GDCResults |
| Set the 'expand' parameter | expand expand.GDCQuery |
| Set facets for a 'GDCQuery' | facet get_facets get_facets.GDCQuery |
| S3 Generic that returns the field description text, if available | field_description field_description.character field_description.GDCQuery |
| Manipulating GDCQuery filters | filter filter.GDCQuery filtering get_filter get_filter.GDCQuery |
| Work with gdc cache directory | gdc_cache gdc_set_cache |
| return gdc-client executable path | gdc_client |
| Get clinical information from GDC | gdc_clinical |
| return a gdc token from file or environment | gdc_token |
| Download GDC files | gdcdata |
| Find matching field names | grep_fields |
| get the name of the id field | id_field id_field.GDCQuery id_field.GDCResults |
| Get the ids associated with a GDC query or response | ids ids.GDCManifest ids.GDCQuery ids.GDCResponse ids.GDCResults |
| Create NCI GDC filters for limiting GDC query results | make_filter |
| Prepare GDC manifest file for bulk download | manifest manifest.GDCcasesResponse manifest.GDCfilesResponse manifest.gdc_files |
| Query GDC for available endpoint fields | mapping |
| Start a query of GDC metadata | annotations cases cnvs cnv_occurrences files GDCQuery genes projects query ssms ssm_occurrences |
| Read DNAcopy results into GRanges object | readDNAcopy |
| Read a single htseq-counts result file. | readHTSeqFile |
| Fetch 'GDCQuery' metadata from GDC | GDCResponse response response.GDCQuery response_all |
| results | results results.GDCQuery results.GDCResponse |
| results_all | results_all results_all.GDCQuery results_all.GDCResponse |
| S3 generic to set GDCQuery fields | select select.GDCQuery |
| Query GDC for data slices | slicing |
| Query the GDC for current status | status |
| Bulk data download | gdc_client_version_validate transfer transfer_help |
| write a manifest data.frame to disk | write_manifest |
