Metadata-Version: 2.1
Name: clinphen
Version: 1.28
Summary: An automatic phenotype extractor
Home-page: http://bejerano.stanford.edu/clinphen/
Author: Cole A. Deisseroth
Author-email: cdeisser@stanford.edu
License: UNKNOWN
Description: #ClinPhen is freely available for academic, nonprofit, and personal use.
        #Licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
        
        #ClinPhen is a tool that automatically extracts phenotypes from clinical notes.
        #PIP VERSION INSTRUCTIONS
        ##To extract phenotypes:
        clinphen <path_to_clinincal_note_file>
        
        ##To see how to use other features:
        clinphen -h
        
        ##We also have a version that parses phenotypes from a large table of notes. You can run it with:
        clinphen_bulk <path_to_table_file> <path_to_output_file>
        
        ##The input file for clinphen_bulk, by default, is a 2-column table delimited by a "|" character. The first column is the patient identifier, the second is the note. It should have the following header:
        "MRN"|"NOTE"
        
        ##To learn more, run:
        clinphen_bulk -h
        
        #STANDARD (NON-PIP) VERSION INSTRUCTIONS
        #Running the ClinPhen GUI on a mac:
        
        #Running the ClinPhen GUI on a non-mac:
        
        #Running the ClinPhen GUI on the command line:
        ##Open the terminal
        ##cd to the ClinPhen directory
        ##Run the following command:
        ./ClinPhenApp
        
        #Running ClinPhen directly on the command line:
        ##Open the terminal
        ##cd to the ClinPhen directory
        ##Run the following command:
        ./clinphen input.txt
        ##Replace "input.txt" with the path to the free-text clinical note file that you want to parse.
        ##You can also run the command line with a custom thesaurus:
        ./clinphen input.txt thesaurus.txt
        ##Replace "thesaurus.txt" with the path to your custom thesaurus, which should be in the format: HPO_ID<tab>Synonym
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
