How could I generate a manifest file with filtering of Race and Ethnicity? | How can I get the number of cases with RNA-Seq data added by date to TCGA project with GenomicDataCommons?
This package is considered a duplicate. The official version of this package is found at:https://bioc.r-universe.dev/GenomicDataCommons
Package: GenomicDataCommons 1.37.0
Sean Davis
GenomicDataCommons: NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Authors:
GenomicDataCommons_1.37.0.tar.gz
GenomicDataCommons_1.37.0.zip(r-4.7)GenomicDataCommons_1.37.0.zip(r-4.6)GenomicDataCommons_1.37.0.zip(r-4.5)
GenomicDataCommons_1.37.0.tgz(r-4.6-any)GenomicDataCommons_1.37.0.tgz(r-4.5-any)
GenomicDataCommons_1.37.0.tar.gz(r-4.7-any)GenomicDataCommons_1.37.0.tar.gz(r-4.6-any)
GenomicDataCommons_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomicDataCommons/json (API)
| # 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
Pkgdown/docs site:https://bioconductor.github.io
On BioConductor:GenomicDataCommons-1.37.0(bioc 3.24)GenomicDataCommons-1.36.0(bioc 3.23)
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
Last updated from:1f1dd57f36. Checks:9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 257 | ||
| source / vignettes | OK | 325 | ||
| linux-release-x86_64 | OK | 264 | ||
| macos-release-arm64 | OK | 143 | ||
| macos-oldrel-arm64 | OK | 161 | ||
| windows-devel | OK | 190 | ||
| windows-release | OK | 190 | ||
| windows-oldrel | OK | 220 | ||
| wasm-release | OK | 186 |
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:askpassBiocGenericsbitbit64clicliprcpp11crayoncurldplyrgenericsGenomicRangesgluehmshttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6rappdirsreadrrlangS4VectorsSeqinfostringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrxml2
Questions and answers from over the years
Last update: 2024-05-15
Started: 2021-08-09
The GenomicDataCommons Package
What is the GDC? | Quickstart | Installation | Check connectivity and status | Find data | Download data | Metadata queries | Clinical data | General metadata queries | Basic design | Usage | Querying metadata | Creating a query | Retrieving results | Fields and Values | Facets and aggregation | Filtering | Authentication | Datafile access and download | Data downloads via the GDC API | Bulk downloads | BAM slicing | Use Cases | Cases | How many cases are there per project_id? | How many cases are included in all TARGET projects? | How many cases are included in all TCGA projects? | What is the breakdown of sample types in TCGA-BRCA? | Fetch all samples in TCGA-BRCA that use "Solid Tissue" as a normal. | Get all TCGA case ids that are female | Get all TCGA-COAD case ids that are NOT female | Get all TCGA cases that are missing gender | Get all TCGA cases that are NOT missing gender | Files | How many of each type of file are available? | Find gene-level RNA-seq quantification files for GBM | Slicing | Get all BAM file ids from TCGA-GBM | Troubleshooting | SSL connection errors | sessionInfo() | Developer notes
Last update: 2024-05-06
Started: 2016-06-20
Working with simple somatic mutations
Background | Workflow | Genes and gene details | ssms | convert to VRanges | OncoPrint
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 |
