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 |