Chromatin Interaction Site Detector
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CISD.sh
CISD_loop.sh
README.md
calculate_fft_by_chr.R
calculate_logisticRegression_by_chr.R
call_peak_by_threshold.R
extract_feature_from_FftAndBed.R
extract_from_bed.R
extract_hic_reads_for_loops2.py
get_hspeaks.R
get_hspeaks_by_chr.R
hspeak2points.pl
loopoverlaploop_report_last6f.pl
pipeline2_SampledMNaseReads_by_chr.sh
pipeline_loop_single_chr.sh
pred2randompair.py
pred_loop_svm.R
readme.pdf
run_CISD_and_loop.sh
site_by_chrTofft1to50_by_chr.R
training2_pred2_by_chr.R
wig2Sd.R
write.table0.R

README.md

CISD and CISD_loop v1.0

This is old version for CISD and CISD_loop, which uses SVM and only a few features to predict loops. For latest version, please see the brance CISD_version_2.0. In version 2.0, 106 features(features from Hi-C contact index, FFT profiles and distance) and 4 models(Random Forest, GBDT, AdaBoost and ExtraTree) are used to predict loops, which greatly improves the arrcuracy of the prediction compared with version 1.0.