Created on 2020-08-18

@author: Chen Fu (http://zzdlab.com/HDFP)

Email: fuchen_0818@163.com. Feel free to contact us if you have any questions.



README for HDFP
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HDFP is a human gene functional network-informed prediction method based on a machine learning algorithm to infer the potential HIV-1 HDFs.



Citing HDFP
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Chen Fu, Shiping Yang, Xiaodi Yang, Xianyi Lian, Yan Huang, Xiaobao Dong and Ziding Zhang (2020) A human gene functional network-informed prediction of HIV-1 host dependency factors. Manuscript submitted.


INSTALL
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Required
1) Python3.6 or newer, https://www.python.org/
2) Python packages
$ pip install -U scikit-learn == 0.21
$ pip install pandas == 0.24
$ pip install numpy == 1.16
$ pip install scipy == 1.3
$ pip install joblib == 0.13


USAGE
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$ tar -zxvf HDFP.tar.gz
$ cd HDFP

python HDFP.py   [-i]  [-o]  [-d]  [-h]
Example: python HDFP.py -i example.id -o example_result -d GIANT_feature_matrix.txt

OPTIONAL ARGUMENTS
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-i     The file contains Entrez Gene ID of test data.
-o     The file contains the result of prediction.
-d     GIANT matrix. Note that if you want to predict, this file must be downloaded from our website. The file size is about 7G.
-h     Print USAGE, DESCRIPTION and ARGUMENT messages.

DESCRIPTION
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Name: HDFP
Version: 1.0
Update Time: 2020-08-18