ORscraper

0.1.1

Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar'

0packages depend

2.2Kdownloads / year

97.8%test coverage

13/13checks pass

Overview

About

Maintained by Samuel GonzálezFirst published 2026-01-162 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("ORscraper", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("SamuelGonzalez0204/ORscraper")

Development version from SamuelGonzalez0204/ORscraper. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-orscraper

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ORscraper

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.11

97.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-19
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
3 OK · 0 NOTE · 0 WARNING · 11 ERROR · 0 FAILURE

Documentation

READMEYes · 258 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 90%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #9,373 · ~6/day · ~182/mo

Releases R versions

Daily download trend is not available in this view yet.

22330 days

1.1K90 days

2.2K1 year

Compare downloads with other packages →

Also on45 r2u

Repository

GitHub ↗ samuelgonzalez0204/orscraper

0Stars

0Forks

0Open issues

0Open PRs

1Releases

11Commits

2Contributors

11 commits · Last activity 2026-03-10

Releases over time

2026-01-17 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/samuelgonzalez0204/orscraper on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Research and citation (1)

CITATION.cff

Show all practices

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (4)

pdftools stringr readxl rentrez

LinkingTo (0)

none

Suggests (5)

testthat rmarkdown knitr mockery spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Samuel González

Author, Maintainer

Authors (1)

Samuel González

Author, Maintainer

Contributors (3)

Antonio Jesus Canepa

Contributor

María González

Contributor

Patricia Saiz

Contributor

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2026-03-11 · current release · diff ↗
0.1.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-16
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 503 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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