Hongyang449/ENCODE_exp

ENCODE TF binding site prediction

The codes for 1.process data 2.train&predict 3.analyze results 4.feature importance 5.plot

background: ENCODE-DREAM

see also: Yuanfang Guan's 1st Place Solution Code

Warning! You need to change the PATH to the data on your own disk before running any of the following codes! (Upgrade: modify the path)

Usage Example (Anchor model):

1. process data

cd TF_exp/data_process/anchor_dnase

./bash.sh

cd ../sequence

./bash.sh

cd ../gencode

./bash.sh

2. train and predict

(1) subsample negative cases

cd TF_exp/data/sample

./bash.sh

(2) prepare training & validation data

cd ../train_test/anchor

./bash.sh

(3) train models

cd ../../../model/anchor

./bash.sh

(4) predict

cd ../../prediction/anchor/

./bash.sh

3. analyze

(1) prepare data for evaluation

cd TF_exp/evaluation/target # gold standard

bash bash.sh

cd ../anchor/ # prediction

./bash.sh

(2) calcualte AUROCs and AUPRCs

cd ../../analysis/

./bash.sh

4. feature importance

cd TF_exp/feature_importance

./bash.sh

5. plot

cd TF_exp/analysis/

Rscript plot_fig1.r