Introduction | Setup | Usage | Examples | Example 1 | Example 2 | Example 3 | Future Work | Differences Between Synapse and cBioPortal Genomic Data
Package: genieBPC 2.2.0
Jessica A. Lavery
genieBPC: Project GENIE BioPharma Collaborative Data Processing Pipeline
The American Association Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) BioPharma Collaborative represents a multi-year, multi-institution effort to build a pan-cancer repository of linked clinico-genomic data. The genomic and clinical data are provided in multiple releases (separate releases for each cancer cohort with updates following data corrections), which are stored on the data sharing platform 'Synapse' <https://www.synapse.org/>. The 'genieBPC' package provides a seamless way to obtain the data corresponding to each release from 'Synapse' and to prepare datasets for analysis.
Authors:
genieBPC_2.2.0.tar.gz
genieBPC_2.2.0.zip(r-4.7-any)genieBPC_2.2.0.zip(r-4.6-any)genieBPC_2.2.0.zip(r-4.5-any)
genieBPC_2.2.0.tgz(r-4.6-any)genieBPC_2.2.0.tgz(r-4.5-any)
genieBPC_2.2.0.tar.gz(r-4.7-any)genieBPC_2.2.0.tar.gz(r-4.6-any)
genieBPC_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genieBPC/json (API)
| # Install 'genieBPC' in R: |
| install.packages('genieBPC', repos = c('https://genie-bpc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/genie-bpc/geniebpc/issues
Pkgdown/docs site:https://genie-bpc.github.io
Datasets:
- cohort_institution - List of Institutions by Cohort
- drug_regimen_list - List of Drug Regimen Names by Cohort
- genie_panels - Genomic Panels Included in GENIE BPC Data
- nsclc_test_data - Simulated fake GENIE BPC data for function examples and tests
- regimen_abbreviations - List of Drug Regimen Abbreviations
- synapse_tables - 'Synapse' table IDs
Last updated from:71f2e1fc3d. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 193 | ||
| source / vignettes | OK | 245 | ||
| linux-release | OK | 178 | ||
| macos-release | OK | 153 | ||
| macos-oldrel | OK | 234 | ||
| windows-devel | OK | 99 | ||
| windows-release | OK | 92 | ||
| windows-oldrel | OK | 83 | ||
| wasm-release | OK | 147 |
Exports:.check_download_path.get_and_query_file_url.get_env.get_synapse_token.is_connected_to_genie.pull_data_by_cohort.resolve_duplicates.verify_pat_workscheck_genie_accesscreate_analytic_cohortdrug_regimen_sunburstpull_data_synapseselect_unique_ngsset_synapse_credentialssynapse_version
Dependencies:askpassbase64encbslibcachemclicpp11curld3rdata.tabledigestdplyrdtplyrevaluatefastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetshttrjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpurrrR6rappdirsrlangrmarkdownsassstringistringrsunburstRsystibbletidyrtidyselecttinytexutf8vctrswithrxfunyaml
Tutorial: pull_data_synapse
Last update: 2026-02-25
Started: 2021-12-17
Tutorial: create_analytic_cohort
Introduction | Setup | Modifying Function Arguments | Example using package test data | Examples using data from pull_data_synapse() | Example 2 | Example 3 | Example 4
Last update: 2025-12-10
Started: 2021-12-17
Tutorial: GENIE BPC Data Structure
AACR Project GENIE | GENIE BPC | GENIE BPC Elements | Patient Characteristics | Cancer Diagnosis | Cancer Diagnosis: BPC Project Cancer | Cancer Diagnosis: Non-BPC Project Cancer | Cancer-Directed Regimen Dataset | Cancer-Directed Radiation Therapy Dataset | PRISSMM Pathology Dataset | PRISSMM Imaging Dataset | PRISSMM Medical Oncologist Assessment Dataset | PRISSMM Tumor Marker Dataset | Cancer Panel Test Dataset | Differences Between Synapse and cBioPortal Genomic Data
Last update: 2025-12-10
Started: 2021-12-17
Tutorial: drug_regimen_sunburst
Introduction | Modifying Function Arguments | Setup | Example
Last update: 2025-08-20
Started: 2021-12-17
Tutorial: select_unique_ngs
Introduction | Modifying Function Arguments | Setup | Examples | Example 1 | Example 2
Last update: 2025-08-20
Started: 2021-12-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check Access to GENIE Data | check_genie_access |
| List of Institutions by Cohort | cohort_institution |
| Select cohort of patients for analysis | create_analytic_cohort |
| List of Drug Regimen Names by Cohort | drug_regimen_list |
| Visualize drug regimen sequences in a sunburst plot | drug_regimen_sunburst |
| Genomic Panels Included in GENIE BPC Data | genie_panels |
| Simulated fake GENIE BPC data for function examples and tests | nsclc_test_data |
| Obtain clinical & genomic data files for GENIE BPC Project | pull_data_synapse |
| List of Drug Regimen Abbreviations | regimen_abbreviations |
| Selecting corresponding unique next generation sequencing reports | select_unique_ngs |
| Connect to 'Synapse' API | set_synapse_credentials |
| 'Synapse' table IDs | synapse_tables |
| Return list of available GENIE BPC data releases | synapse_version |