https://www.ncbi.nlm.nih.gov/clinvar/> to enrich extracted data.">

ORscraper: Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar' (original) (raw)

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 ORCID iD [aut, cre], Antonio Jesus CanepaORCID iD [ctb], Patricia Saiz ORCID iD [ctb], María González ORCID iD [ctb]
Maintainer: Samuel González
BugReports: https://github.com/SamuelGonzalez0204/ORscraper/issues
License: MIT + file
URL: https://github.com/SamuelGonzalez0204/ORscraper
NeedsCompilation: no
SystemRequirements: poppler-cpp (>= 0.73)
Language: en-US
Materials: README, NEWS
CRAN checks: ORscraper results [issues need fixing before 2026-03-31]

Documentation:

Downloads:

Linking:

Please use the canonical formhttps://CRAN.R-project.org/package=ORscraperto link to this page.