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.

Version: 1.1.1
Depends: R (≥ 3.4)
Imports: cli (≥ 2.5.0), dplyr (≥ 1.0.6), dtplyr (≥ 1.1.0), httr, jsonlite, purrr (≥ 0.3.4), rlang (≥ 1.0.0), stringr (≥ 1.4.0), sunburstR, tibble (≥ 3.1.2), tidyr
Suggests: covr (≥ 3.5.1), ggplot2 (≥ 3.3.5), gt (≥ 0.3.0), gtsummary (≥ 1.5.2), knitr (≥ 1.33), magrittr (≥ 2.0.1), plotly (≥ 4.10.0), rmarkdown (≥ 2.8), testthat (≥ 3.0.0), markdown, spelling
Published: 2024-03-29
DOI: NA
Author: Jessica A. Lavery ORCID iD [aut, cre], Michael A. Curry ORCID iD [aut], Samantha Brown ORCID iD [aut], Karissa Whiting ORCID iD [aut], Hannah Fuchs ORCID iD [aut], Axel Martin [aut], Daniel D. Sjoberg ORCID iD [ctb]
Maintainer: Jessica A. Lavery <laveryj at mskcc.org>
BugReports: https://github.com/GENIE-BPC/genieBPC/issues
License: MIT + file LICENSE
URL: https://genie-bpc.github.io/genieBPC/
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: genieBPC results

Documentation:

Reference manual: genieBPC.pdf
Vignettes: Tutorial: GENIE BPC Data Structure
Tutorial: create_analytic_cohort
Tutorial: drug_regimen_sunburst
Tutorial: pull_data_synapse
Tutorial: select_unique_ngs

Downloads:

Package source: genieBPC_1.1.1.tar.gz
Windows binaries: r-devel: genieBPC_1.1.1.zip, r-release: genieBPC_1.1.1.zip, r-oldrel: genieBPC_1.1.1.zip
macOS binaries: r-release (arm64): genieBPC_1.1.1.tgz, r-oldrel (arm64): genieBPC_1.1.1.tgz, r-release (x86_64): genieBPC_1.1.1.tgz, r-oldrel (x86_64): genieBPC_1.1.1.tgz
Old sources: genieBPC archive

Linking:

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