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

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Documentation for package ‘ORscraper’ version 0.1.1

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

classify_biopsy	Determine the type of biopsy from identifiers
extract_chip_id	Extract numeric identifiers from file names
extract_fusions	Extract fusion variants from text
extract_intermediate_values	Extract intermediate values from text lines
extract_values_from_tables	Extract values from tables within text
extract_values_start_end	Extract values from start or end patterns
extract_variable	Extract variable value from text lines
filter_pathogenic_only	Filter for pathogenic results only
narrow_text	Extract a subset of text based on start and end patterns
read_pdf_content	Read content from a PDF file
read_pdf_files	Read all PDF files in a directory
search_ncbi_clinvar	Search for pathogenicity information in NCBI ClinVar
search_value	Search for a specific value in text lines