Package: cbioportalR 1.1.0.9000
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_1.1.0.9000.tar.gz
cbioportalR_1.1.0.9000.zip(r-4.5)cbioportalR_1.1.0.9000.zip(r-4.4)cbioportalR_1.1.0.9000.zip(r-4.3)
cbioportalR_1.1.0.9000.tgz(r-4.4-any)cbioportalR_1.1.0.9000.tgz(r-4.3-any)
cbioportalR_1.1.0.9000.tar.gz(r-4.5-noble)cbioportalR_1.1.0.9000.tar.gz(r-4.4-noble)
cbioportalR_1.1.0.9000.tgz(r-4.4-emscripten)cbioportalR_1.1.0.9000.tgz(r-4.3-emscripten)
cbioportalR.pdf |cbioportalR.html✨
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
- impact_gene_info - IMPACT Gene Meta Data
Last updated 3 days agofrom:04d7dfec09. Checks:OK: 5 NOTE: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 19 2024 |
R-4.5-win | NOTE | Nov 19 2024 |
R-4.5-linux | NOTE | Nov 19 2024 |
R-4.4-win | OK | Nov 19 2024 |
R-4.4-mac | OK | Nov 19 2024 |
R-4.3-win | OK | Nov 19 2024 |
R-4.3-mac | OK | Nov 19 2024 |
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:askpassclicpp11curldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6rlangstringistringrsystibbletidyrtidyselectutf8vctrswithr
Internal Structure & Guiding Principles
Rendered frominternal-structure.Rmd
usingknitr::rmarkdown
on Nov 19 2024.Last update: 2022-07-14
Started: 2022-03-15
Overview of Data Retrieval Workflow
Rendered fromoverview-of-workflow.Rmd
usingknitr::rmarkdown
on Nov 19 2024.Last update: 2024-11-19
Started: 2022-03-15