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:Jessica A. Lavery [aut, cre], Michael A. Curry [aut], Samantha Brown [aut], Karissa Whiting [aut], Yufei Deng [aut], Hannah Fuchs [ctb], Axel Martin [ctb], Daniel D. Sjoberg [ctb]

genieBPC_2.2.0.tar.gz
genieBPC_2.2.0.zip(r-4.7)genieBPC_2.2.0.zip(r-4.6)genieBPC_2.2.0.zip(r-4.5)
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:

On CRAN:

Conda:

7.72 score 10 stars 30 scripts 736 downloads 15 exports 51 dependencies

Last updated from:71f2e1fc3d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK188
source / vignettesOK229
linux-release-x86_64OK212
macos-release-arm64OK116
macos-oldrel-arm64OK129
windows-develOK114
windows-releaseOK106
windows-oldrelOK141
wasm-releaseOK160

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
Introduction | Setup | Usage | Examples | Example 1 | Example 2 | Example 3 | Future Work | Differences Between Synapse and cBioPortal Genomic Data
Rendered frompull_data_synapse_vignette.Rmdusingknitr::rmarkdown

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
Rendered fromcreate_analytic_cohort_vignette.Rmdusingknitr::rmarkdown

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
Rendered fromclinical_data_structure_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-12-10
Started: 2021-12-17

Tutorial: drug_regimen_sunburst
Introduction | Modifying Function Arguments | Setup | Example
Rendered fromdrug_regimen_sunburst_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-08-20
Started: 2021-12-17

Tutorial: select_unique_ngs
Introduction | Modifying Function Arguments | Setup | Examples | Example 1 | Example 2
Rendered fromselect_unique_ngs_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-08-20
Started: 2021-12-17