Man pages for Bioconductor/GenomicDataCommons
NIH / NCI Genomic Data Commons Access

available_expandReturn valid values for "expand"
available_fieldsS3 Generic to return all GDC fields
available_valuesFind common values for a GDC field
constantsEndpoints and Parameters
countprovide count of records in a 'GDCQuery'
default_fieldsS3 Generic to return default GDC fields
dot-htseq_importerImport multiple files of HTSeq-counts format
entity_nameGet the entity name from a GDCQuery object
expandSet the 'expand' parameter
facetingSet facets for a 'GDCQuery'
filteringManipulating GDCQuery filters
gdc_cacheWork with gdc cache directory
gdc_clientreturn gdc-client executable path
gdc_clinicalGet clinical information from GDC
gdcdataDownload GDC files
gdc_rnaseqGet RNA-seq quantification from the NCI GDC.
gdc_tokenreturn a gdc token from file or environment
GenomicDataCommonsncigdc: A package for computating the notorious bar...
grep_fieldsFind matching field names
id_fieldget the name of the id field
idsGet the ids associated with a GDC query or response
make_filterCreate NCI GDC filters for limiting GDC query results
manifestPrepare GDC manifest file for bulk download
mappingQuery GDC for available endpoint fields
queryStart a query of GDC metadata
readDNAcopyRead DNAcopy results into GRanges object
readHTSeqFileRead a single htseq-counts result file.
responseFetch 'GDCQuery' metadata from GDC
selectS3 generic to set GDCQuery fields
slicingQuery GDC for data slices
statusQuery the GDC for current status
transferBulk data download
write_manifestwrite a manifest data.frame to disk
Bioconductor/GenomicDataCommons documentation built on Nov. 6, 2019, 7:03 a.m.