Instructions: 1. Download everything to a directory in Linux/Unix 2. Install Eisen's cluster software (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm) 3. Make sure R and Perl are pre-installed 4. Run it like this % Perl WC_wapper_SCCA_final.pl positve_target.txt all_transcription_factor.txt positive_guide_genes.txt Since it usually takes 5~20 h to run, it is better to run your ananlysis in background like this %nohup WC_wapper_SCCA_final.pl positve_target.txt all_transcription_factor.txt positive_guide_genes.txt & Alternatively you can use screen to detach your terminal from server after the job is submitted. We provided two sets of sample data sets for testing. Codes: A. WC_wapper_SCCA_final.pl main Perl script B. ascca_parser.pl parser C. cluster_parse.pl parser D. cal_scca_freq.pl calculate frequency for each TF discovered E. ascca_CV_gamma_command_line.R main ASCCA code F. scca_command_line.R SCCA code that not used for the package, a gift. You can use it for standalone analysis G. func.R required by ASCCA and SCCA A set of test data Salt_stress_allTF1640.txt Salt_stress_positive_TF13_guide.txt Salt_stress_target_Gene157_bait.txt How to run? %nohup WC_wapper_SCCA_final.pl Salt_stress_target_Gene157_bait.txt Salt_stress_allTF1640.txt Salt_stress_positive_TF13_guide.txt & Check the output next day.