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:Karissa Whiting [aut, cre]

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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'))

Peer review:

Bug tracker:https://github.com/karissawhiting/cbioportalr/issues

Datasets:

On CRAN:

6.66 score 19 stars 20 scripts 298 downloads 39 exports 28 dependencies

Last updated 22 days agofrom:09462e77e3. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 15 2024
R-4.5-winNOTEOct 15 2024
R-4.5-linuxNOTEOct 15 2024
R-4.4-winOKOct 15 2024
R-4.4-macOKOct 15 2024
R-4.3-winOKOct 15 2024
R-4.3-macOKOct 15 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_infoset_cbioportal_dbtest_cbioportal_db

Dependencies:askpassclicpp11curldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6rlangstringistringrsystibbletidyrtidyselectutf8vctrswithr

Internal Structure & Guiding Principles

Rendered frominternal-structure.Rmdusingknitr::rmarkdownon Oct 15 2024.

Last update: 2022-07-14
Started: 2022-03-15

Overview of Data Retrieval Workflow

Rendered fromoverview-of-workflow.Rmdusingknitr::rmarkdownon Oct 15 2024.

Last update: 2023-10-05
Started: 2022-03-15

Readme and manuals

Help Manual

Help pageTopics
Get all available clinical attribute IDs for a studyavailable_clinical_attributes
Get Available Gene Panels For a Databaseavailable_gene_panels
Get All Patient IDs in a Studyavailable_patients
Get Available Genomic Profiles For a Study or Databaseavailable_profiles
Get All Sample Lists Available For a Studyavailable_sample_lists
Get All Sample IDs in a Studyavailable_samples
Get Metadata on All Available Studies in a Databaseavailable_studies
Get Gene Name Alias for a Given Hugo Symbolget_alias
Get cBioPortal Access Tokenget_cbioportal_token
Get clinical data by attribute, study ID and patient IDget_clinical_by_patient
Get clinical data by attribute, study ID and sample IDget_clinical_by_sample
Get all available clinical data for a specified studyget_clinical_by_study
Get CNA By Sample IDget_cna_by_sample
Get CNA By Studyget_cna_by_study
Get Entrez Gene ID for a given set of Hugo Symbolsget_entrez_id
Get Fusions By Sample IDget_fusions_by_sample get_structural_variants_by_sample
Get Fusions By Studyget_fusions_by_study get_structural_variants_by_study
Retrieve Genes Included For a Specified Panel IDget_gene_panel
Get A List of Genes for a Specified Databaseget_genes
Get All Genomic Information By Sample IDsget_genetics_by_sample
Get All Genomic Information By Studyget_genetics_by_study
Get Hugo Symbol for a given set of Entrez IDsget_hugo_symbol
Get Mutations By Sample IDget_mutations_by_sample
Get Mutations By Study IDget_mutations_by_study
Get Gene Panel by study ID and sample IDget_panel_by_sample
Get sample IDs for a given set of patient IDsget_samples_by_patient
Get Copy Number Segmentation Data By Sample IDget_segments_by_sample
Get Copy Number Segmentation Data By Studyget_segments_by_study
Get Metadata on All Available Studies in Database or a Specified Studyget_study_info
IMPACT Gene Meta Dataimpact_gene_info
Connect to cBioPortal DBset_cbioportal_db
Test the Database Connection Anytime During your R Sessiontest_cbioportal_db