Package: ORscraper 0.1.1
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.
Authors:
ORscraper_0.1.1.tar.gz
ORscraper_0.1.1.zip(r-4.7)ORscraper_0.1.1.zip(r-4.6)ORscraper_0.1.1.zip(r-4.5)
ORscraper_0.1.1.tgz(r-4.6-any)ORscraper_0.1.1.tgz(r-4.5-any)
ORscraper_0.1.1.tar.gz(r-4.7-any)ORscraper_0.1.1.tar.gz(r-4.6-any)
ORscraper_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ORscraper/json (API)
NEWS
| # Install 'ORscraper' in R: |
| install.packages('ORscraper', repos = c('https://samuelgonzalez0204.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/samuelgonzalez0204/orscraper/issues
Last updated from:30ef489dba. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 137 | ||
| source / vignettes | OK | 220 | ||
| linux-release-x86_64 | NOTE | 128 | ||
| macos-release-arm64 | NOTE | 121 | ||
| macos-oldrel-arm64 | NOTE | 144 | ||
| windows-devel | NOTE | 89 | ||
| windows-release | NOTE | 86 | ||
| windows-oldrel | NOTE | 82 | ||
| wasm-release | OK | 120 |
Exports:classify_biopsyextract_chip_idextract_fusionsextract_intermediate_valuesextract_values_from_tablesextract_values_start_endfilter_pathogenic_onlyread_pdf_contentread_pdf_filessearch_ncbi_clinvar
Dependencies:askpasscellrangerclicpp11crayoncurlgluehmshttrjsonlitelifecyclemagrittrmimeopensslpdftoolspillarpkgconfigprettyunitsprogressqpdfR6Rcppreadxlrematchrentrezrlangstringistringrsystibbleutf8vctrsXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Determine the type of biopsy from identifiers | classify_biopsy |
| Extract numeric identifiers from file names | extract_chip_id |
| Extract fusion variants from text | extract_fusions |
| Extract intermediate values from text lines | extract_intermediate_values |
| Extract values from tables within text | extract_values_from_tables |
| Extract values from start or end patterns | extract_values_start_end |
| Extract variable value from text lines | extract_variable |
| Filter for pathogenic results only | filter_pathogenic_only |
| Extract a subset of text based on start and end patterns | narrow_text |
| Read content from a PDF file | read_pdf_content |
| Read all PDF files in a directory | read_pdf_files |
| Search for pathogenicity information in NCBI ClinVar | search_ncbi_clinvar |
| Search for a specific value in text lines | search_value |
