Package: genieBPC 2.0.1
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_2.0.1.tar.gz
genieBPC_2.0.1.zip(r-4.5)genieBPC_2.0.1.zip(r-4.4)genieBPC_2.0.1.zip(r-4.3)
genieBPC_2.0.1.tgz(r-4.4-any)genieBPC_2.0.1.tgz(r-4.3-any)
genieBPC_2.0.1.tar.gz(r-4.5-noble)genieBPC_2.0.1.tar.gz(r-4.4-noble)
genieBPC_2.0.1.tgz(r-4.4-emscripten)genieBPC_2.0.1.tgz(r-4.3-emscripten)
genieBPC.pdf |genieBPC.html✨
genieBPC/json (API)
NEWS
| # 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
- 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 2 months agofrom:37a8799b32. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win | OK | Sep 13 2024 |
| R-4.5-linux | OK | Sep 13 2024 |
| R-4.4-win | OK | Sep 13 2024 |
| R-4.4-mac | OK | Sep 13 2024 |
| R-4.3-win | OK | Sep 13 2024 |
| R-4.3-mac | OK | Sep 13 2024 |
Exports:.check_download_path.get_and_query_file_url.get_env.get_synapse_token.get_token_by_pat.get_token_by_username.is_connected_to_genie.pull_data_by_cohort.resolve_duplicatescheck_genie_accesscreate_analytic_cohortdrug_regimen_sunburstpull_data_synapseselect_unique_ngsset_synapse_credentialssynapse_version
Dependencies:askpassbase64encbslibcachemclicpp11curld3rdata.tabledigestdplyrdtplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetshttrjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpurrrR6rappdirsrlangrmarkdownsassstringistringrsunburstRsystibbletidyrtidyselecttinytexutf8vctrswithrxfunyaml
Tutorial: create_analytic_cohort
Rendered fromcreate_analytic_cohort_vignette.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-07-03
Started: 2021-12-17
Tutorial: drug_regimen_sunburst
Rendered fromdrug_regimen_sunburst_vignette.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-07-03
Started: 2021-12-17
Tutorial: GENIE BPC Data Structure
Rendered fromclinical_data_structure_vignette.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-07-10
Started: 2021-12-17
Tutorial: pull_data_synapse
Rendered frompull_data_synapse_vignette.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-07-10
Started: 2021-12-17
Tutorial: select_unique_ngs
Rendered fromselect_unique_ngs_vignette.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-07-03
Started: 2021-12-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check Access to GENIE Data | check_genie_access |
| 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 |
