Package: cbioportalR 1.1.1
cbioportalR: Browse and Query Clinical and Genomic Data from cBioPortal
Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly functions that wrap 'cBioPortal's' existing API endpoints <https://www.cbioportal.org/api/swagger-ui/index.html>. Users can browse and query genomic data on mutations, copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'), microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study). See <https://www.cbioportal.org/> and Gao et al., (2013) <doi:10.1126/scisignal.2004088> for more information on the cBioPortal web resource.
Authors:
cbioportalR_1.1.1.tar.gz
cbioportalR_1.1.1.zip(r-4.7)cbioportalR_1.1.1.zip(r-4.6)cbioportalR_1.1.1.zip(r-4.5)
cbioportalR_1.1.1.tgz(r-4.6-any)cbioportalR_1.1.1.tgz(r-4.5-any)
cbioportalR_1.1.1.tar.gz(r-4.7-any)cbioportalR_1.1.1.tar.gz(r-4.6-any)
cbioportalR_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cbioportalR/json (API)
NEWS
| # Install 'cbioportalR' in R: |
| install.packages('cbioportalR', repos = c('https://karissawhiting.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/karissawhiting/cbioportalr/issues
Pkgdown/docs site:https://www.karissawhiting.com
- impact_gene_info - IMPACT Gene Meta Data
Last updated from:f565f88bc4. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 142 | ||
| source / vignettes | OK | 167 | ||
| linux-release-x86_64 | OK | 130 | ||
| macos-release-arm64 | OK | 155 | ||
| macos-oldrel-arm64 | OK | 206 | ||
| windows-devel | OK | 124 | ||
| windows-release | OK | 99 | ||
| windows-oldrel | OK | 107 | ||
| wasm-release | OK | 116 |
Exports:.get_clinical_by_list_item.get_clinical_pat_by_list_item.get_data_by_sample.get_data_by_study%>%available_clinical_attributesavailable_gene_panelsavailable_patientsavailable_profilesavailable_sample_listsavailable_samplesavailable_studiescbp_apiget_aliasget_cbioportal_tokenget_clinical_by_patientget_clinical_by_sampleget_clinical_by_studyget_cna_by_sampleget_cna_by_studyget_entrez_idget_fusions_by_sampleget_fusions_by_studyget_gene_panelget_genesget_genetics_by_sampleget_genetics_by_studyget_hugo_symbolget_mutations_by_sampleget_mutations_by_studyget_panel_by_sampleget_samples_by_patientget_segments_by_sampleget_segments_by_studyget_structural_variants_by_sampleget_structural_variants_by_studyget_study_infolookup_idset_cbioportal_dbtest_cbioportal_db
Dependencies:askpassclicpp11curldplyrgenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6rlangstringistringrsystibbletidyrtidyselectutf8vctrswithr
Internal Structure & Guiding Principles
Rendered frominternal-structure.Rmdusingknitr::rmarkdownon May 19 2026.Last update: 2022-07-14
Started: 2022-03-15
Overview of Data Retrieval Workflow
Rendered fromoverview-of-workflow.Rmdusingknitr::rmarkdownon May 19 2026.Last update: 2024-11-19
Started: 2022-03-15
