Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 6 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.4%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: progenetix
- Language: R
- Default Branch: devel
- Size: 10.5 MB
Statistics
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
pgxRpi
Welcome to our R wrapper package for Progenetix REST API that leverages the capabilities of Beacon v2 specification. Please note that a stable internet connection is required for the query functionality. This package is aimed to simplify the process of accessing oncogenomic data from Progenetix database via the Beacon v2 API with some extensions (BeaconPlus). Although pgxRpi is designed primarily for Progenetix, it is also compatible with other resources that implement the Beacon v2 API.
You can install this package using either of the following methods:
From Github for the latest development version
r
if (!require("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("progenetix/pgxRpi")
From Bioconductor
Note: this requires Bioconductor release version ≥ 3.19. We strongly recommend using the latest Bioconductor release to ensure compatibility and access to the most up-to-date features.
r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pgxRpi")
For details on accessing biosample or individual information, get started from the vignette Introduction1load_metadata.
To access CNV variant data, get started from this vignette Introduction2query_variants.
To access CNV frequency data, get started from this vignette Introduction3accesscnvfrequency.
For processing local ".pgxseg" files, get started from this vignette Introduction4process_pgxseg.
If you encounter problems, try to reinstall the latest version. If reinstallation doesn't help, please contact us.
Citation
If you use pgxRpi in your research, please cite our associated publication:
Zhao H, Baudis M (2025). pgxRpi: an R/bioconductor package for user-friendly access to the Beacon v2 API. Bioinformatics Advances, 5(1): vbaf172. doi: 10.1093/bioadv/vbaf172
Owner
- Name: Progenetix - genomic aberrations in cancer
- Login: progenetix
- Kind: organization
- Location: Zürich, Switzerland
- Website: www.progenetix.org
- Repositories: 23
- Profile: https://github.com/progenetix
GitHub Events
Total
- Push event: 17
- Create event: 2
Last Year
- Push event: 17
- Create event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| hangjiaz | z****4@g****m | 126 |
| Hangjia Zhao | 5****z@u****m | 9 |
| A Wokaty | a****y@s****u | 2 |
| Hangjia Zhao | z****a@s****h | 2 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y@u****m | 2 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 4,084 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 11
- Total maintainers: 1
bioconductor.org: pgxRpi
R wrapper for Progenetix
- Homepage: https://github.com/progenetix/pgxRpi
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/pgxRpi/inst/doc/pgxRpi.pdf
- License: Artistic-2.0
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Latest release: 1.4.3
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.2 depends
- attempt * imports
- circlize * imports
- dplyr * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- lubridate * imports
- methods * imports
- plyr * imports
- rjson * imports
- survival * imports
- survminer * imports
- utils * imports
- BiocStyle * suggests
- RColorBrewer * suggests
- httr * suggests
- knitr * suggests
- pheatmap * suggests
- rmarkdown * suggests
- testthat * suggests