NIH / NCI Genomic Data Commons Access
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Documentation for package ‘GenomicDataCommons’ version 1.33.1
Help Pages
| GenomicDataCommons-package | GenomicDataCommons: A package for interfacing with the NCI GDC |
| aggregations | aggregations |
| aggregations.GDCQuery | aggregations |
| aggregations.GDCResponse | aggregations |
| annotations | Start a query of GDC metadata |
| available_expand | Return valid values for "expand" |
| available_expand.character | Return valid values for "expand" |
| available_expand.GDCQuery | Return valid values for "expand" |
| available_fields | S3 Generic to return all GDC fields |
| available_fields.character | S3 Generic to return all GDC fields |
| available_fields.GDCQuery | S3 Generic to return all GDC fields |
| available_values | Find common values for a GDC field |
| cases | Start a query of GDC metadata |
| cnvs | Start a query of GDC metadata |
| cnv_occurrences | Start a query of GDC metadata |
| count | provide count of records in a 'GDCQuery' |
| count.GDCQuery | provide count of records in a 'GDCQuery' |
| count.GDCResponse | provide count of records in a 'GDCQuery' |
| default_fields | S3 Generic to return default GDC fields |
| default_fields.character | S3 Generic to return default GDC fields |
| default_fields.GDCQuery | S3 Generic to return default GDC fields |
| entity_name | Get the entity name from a GDCQuery object |
| entity_name.GDCQuery | Get the entity name from a GDCQuery object |
| entity_name.GDCResults | Get the entity name from a GDCQuery object |
| expand | Set the 'expand' parameter |
| expand.GDCQuery | Set the 'expand' parameter |
| facet | Set facets for a 'GDCQuery' |
| field_description | S3 Generic that returns the field description text, if available |
| field_description.character | S3 Generic that returns the field description text, if available |
| field_description.GDCQuery | S3 Generic that returns the field description text, if available |
| files | Start a query of GDC metadata |
| filter | Manipulating GDCQuery filters |
| filter.GDCQuery | Manipulating GDCQuery filters |
| filtering | Manipulating GDCQuery filters |
| gdcdata | Download GDC files |
| GDCQuery | Start a query of GDC metadata |
| GDCResponse | Fetch 'GDCQuery' metadata from GDC |
| gdc_cache | Work with gdc cache directory |
| gdc_client | return gdc-client executable path |
| gdc_client_version_validate | Bulk data download |
| gdc_clinical | Get clinical information from GDC |
| gdc_set_cache | Work with gdc cache directory |
| gdc_token | return a gdc token from file or environment |
| genes | Start a query of GDC metadata |
| GenomicDataCommons | GenomicDataCommons: A package for interfacing with the NCI GDC |
| get_facets | Set facets for a 'GDCQuery' |
| get_facets.GDCQuery | Set facets for a 'GDCQuery' |
| get_filter | Manipulating GDCQuery filters |
| get_filter.GDCQuery | Manipulating GDCQuery filters |
| grep_fields | Find matching field names |
| ids | Get the ids associated with a GDC query or response |
| ids.GDCManifest | Get the ids associated with a GDC query or response |
| ids.GDCQuery | Get the ids associated with a GDC query or response |
| ids.GDCResponse | Get the ids associated with a GDC query or response |
| ids.GDCResults | Get the ids associated with a GDC query or response |
| id_field | get the name of the id field |
| id_field.GDCQuery | get the name of the id field |
| id_field.GDCResults | get the name of the id field |
| make_filter | Create NCI GDC filters for limiting GDC query results |
| manifest | Prepare GDC manifest file for bulk download |
| manifest.GDCcasesResponse | Prepare GDC manifest file for bulk download |
| manifest.GDCfilesResponse | Prepare GDC manifest file for bulk download |
| manifest.gdc_files | Prepare GDC manifest file for bulk download |
| mapping | Query GDC for available endpoint fields |
| projects | Start a query of GDC metadata |
| query | Start a query of GDC metadata |
| readDNAcopy | Read DNAcopy results into GRanges object |
| readHTSeqFile | Read a single htseq-counts result file. |
| response | Fetch 'GDCQuery' metadata from GDC |
| response.GDCQuery | Fetch 'GDCQuery' metadata from GDC |
| response_all | Fetch 'GDCQuery' metadata from GDC |
| results | results |
| results.GDCQuery | results |
| results.GDCResponse | results |
| results_all | results_all |
| results_all.GDCQuery | results_all |
| results_all.GDCResponse | results_all |
| select | S3 generic to set GDCQuery fields |
| select.GDCQuery | S3 generic to set GDCQuery fields |
| slicing | Query GDC for data slices |
| ssms | Start a query of GDC metadata |
| ssm_occurrences | Start a query of GDC metadata |
| status | Query the GDC for current status |
| transfer | Bulk data download |
| transfer_help | Bulk data download |
| write_manifest | write a manifest data.frame to disk |