dce's Introduction

Cite

If you make use of this code in your own work, please cite our paper:

@inproceedings{DCE,
  title={Identification of Cancer Development Related Pathways Based on Co-Expression Analyses},
  author={Hongyang Jiang, Zhihang Wang, Chaoyi Yin, Peishuo Sun, Ying Xu, and Huiyan Sun},
  booktitle={2020 IEEE International Conference on Bioinformatics and Biomedicine},
  year={2020}
}

step1

# the code is written by python, version=3.6.9
# calculate co-expression by Spearman

# input data is in ./DCE_BIBM2020/dataset/
# output data in ./DCE_BIBM2020/cache/result_1to23/    will used in step2 and step3

cd ./DCE_BIBM2020/step1_calculate_Spearman
	nohup python3 -u -W ignore run_this.py -d='COAD' > _log_COAD.txt 2>&1 & 
	nohup python3 -u -W ignore run_this.py -d='KIRC' > _log_KIRC.txt 2>&1 & 
	nohup python3 -u -W ignore run_this.py -d='LUAD' > _log_LUAD.txt 2>&1 & 
	nohup python3 -u -W ignore run_this.py -d='THCA' > _log_THCA.txt 2>&1 &

step2

# the code is written by python, version=3.6.9
# calculate the largest component and statistic some result of the network

# input data is in ./DCE_BIBM2020/cache/result_1to23/
# output data in ./DCE_BIBM2020/cache/result_2to3/     will used in step3
# output data in ./DCE_BIBM2020/cache/result_2/        is some statistic of the network

cd ./DCE_BIBM2020/step2_get_max_component
	nohup python3 -u -W ignore run_this.py > _log.txt 2>&1 &

step3

# the code is written by R, version=4.0.2

# input data is in ./DCE_BIBM2020/cache/result_2to3/
# output data in ./DCE_BIBM2020/cache/result_3/

cd ./DCE_BIBM2020/step3_analysis_BCCCDC/main
	nohup Rscript run_this.R > _log.txt 2>&1 &

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