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: | 2.0.1 |
| 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: | 2024-07-11 |
| DOI: | 10.32614/CRAN.package.genieBPC |
| Author: | Jessica A. Lavery 
[aut, cre],
Michael A. Curry
[aut],
Samantha Brown
[aut],
Karissa Whiting
[aut],
Hannah Fuchs
[aut],
Axel Martin [aut],
Daniel D. Sjoberg
[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.html , genieBPC.pdf |
| Vignettes: |
Tutorial: GENIE BPC Data Structure (source, R code) Tutorial: create_analytic_cohort (source, R code) Tutorial: drug_regimen_sunburst (source, R code) Tutorial: pull_data_synapse (source, R code) Tutorial: select_unique_ngs (source, R code) |
Downloads:
| Package source: | genieBPC_2.0.1.tar.gz |
| Windows binaries: | r-devel: genieBPC_2.0.1.zip, r-release: genieBPC_2.0.1.zip, r-oldrel: genieBPC_2.0.1.zip |
| macOS binaries: | r-release (arm64): genieBPC_2.0.1.tgz, r-oldrel (arm64): genieBPC_2.0.1.tgz, r-release (x86_64): genieBPC_2.0.1.tgz, r-oldrel (x86_64): genieBPC_2.0.1.tgz |
| Old sources: | genieBPC archive |
Linking:
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