README

Standalone version of CarcinoHPVPred is consist of scripts and models written and tested with perl-5 and python-3.9.9.
It works with linux OS only.
This tool can be used to predict the carcinogenic nature of new or already available HPV strains. This tool uses genomic information from two HPV core genes E2 and E6.

Dependencies:
perl-5
python-3.9.9
sklearn: 1.0.2
numpy: 1.23.1
scipy: 1.9.0
pandas: 1.4.3
matplotlib: 3.5.2
joblib: 1.1.0


Installation:

unzip CarcinoHPVPred.zip

To run program simply type:

cd CarcinoHPVPred/

perl CarcinoHPVPred.pl abc.fasta modelName type_of_input

abc.fasta = genome or predicted genes in fasta format

modelName = logistic_regression or svm or knn or lda

type_of_input = full_genome or E2_E6 or E6