Codes to reproduce the analysis from publication DOI: 10.1158/2159-8290.CD-24-1853. Raw and processed data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE312368
Please refer as well to Matherial and Methods of the paper to have additional details of the softwares used. Here are the main:
- HiC-Pro 3.1.0
- HiCExplorer 3.7.4
- domaincaller 0.1.0
- cooltools 0.5.4
- Peakachu 2.3
- R/GENOVA 1.0.0
- R/Diffloop 1.22.0
- hichipper 0.7.8
- ABC-Enhancer-Gene-Prediction 1.1.2 (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction)
- STAR 2.7.7a
- trimgalore 0.6.6
- pipseeker 3.3.0
If you have any trouble, contact me, I am very responsive ;)!