ORscraper: Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar'
Clinical reports generated by 'Oncomine Reporter' software contain critical data in unstructured PDF format, making manual extraction time-consuming and error-prone. 'ORscraper' provides a coherent suite of functions to automate this process, allowing researchers to parse reports, identify key biomarkers, extract genetic variant tables, and filter results. It also integrates with the NCBI 'ClinVar' API <https://www.ncbi.nlm.nih.gov/clinvar/> to enrich extracted data.
| Version: | 0.1.0 |
| Depends: | R (≥ 4.0.0) |
| Imports: | pdftools, stringr, readxl, rentrez |
| Suggests: | testthat (≥ 3.0.0), rmarkdown, knitr, mockery, spelling |
| Published: | 2026-01-16 |
| DOI: | 10.32614/CRAN.package.ORscraper |
| Author: | Samuel González 
[aut, cre],
Antonio Jesus Canepa
[ctb],
Patricia Saiz
[ctb],
María González
[ctb] |
| Maintainer: | Samuel González <samugonz0204 at gmail.com> |
| BugReports: | https://github.com/SamuelGonzalez0204/ORscraper/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/SamuelGonzalez0204/ORscraper |
| NeedsCompilation: | no |
| SystemRequirements: | poppler-cpp (>= 0.73) |
| Language: | en-US |
| Materials: | README, NEWS |
| CRAN checks: | ORscraper results |
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