ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features.

"the rad21 chip-seq data for the four cell lines can be downloaded from ncbi geo: gsm935332 (gm12878 cell line) gsm935319 (k562 cell line) gsm935379 (h1 cell line) and gsm935647 (hepg2 cell line) [ 29 ].; the h3k27ac chip-seq data for the four cell lines can be downloaded from ncbi geo: gsm733771 (gm12878 cell line) gsm733656 (k562 cell line) gsm733718 (h1 cell line) and gsm733743 (hepg2 cell line) [ 29 ].; the h3k27me3 chip-seq data for the four cell lines can be downloaded from ncbi geo: gsm733758 (gm12878 cell line) gsm733658 (k562 cell line) gsm733748 (h1 cell line) and gsm733754 (hepg2 cell line).; the ctcf chip-seq peaks can be downloaded from ncbi geo: gsm935611 (gm12878 cell line) gsm935407 (k562 cell line) gsm733672 (h1 cell line) gsm733645 (hepg2 cell line) gse105500 (lncap cell line) gse175278 (h9 cell line) and gsm1006878 (mcf7 cell line).; the micro-c data of the h1 cell line can be downloaded from the 4dn data portal with the accession number 4dnfi9gmp2j8 [ 38 ]. it has also been deposited at zenodo with doi 10 5281/zenodo 10364968 [ 54 ]. we chose the k562 cell line because its training data for 3dpredictor is available on the github page of the method ( https://github com/labdevgen/3dpredictor/tree/master )."

"we chose the k562 cell line because its training data for 3dpredictor is available on the github page of the method ( https://github com/labdevgen/3dpredictor/tree/master ).; source code of chipr with a detailed readme file is freely available under the gnu general public license version 2 (gplv2) at https://git biohpc swmed edu/s206442/chipr [ 53 ]."

"Declarations Ethics approval and consent to participateNot applicable for this study. Competing interestsThe authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests."

"Funding RSM acknowledges funding support from the NCI/NIH (grant R01CA245294), CPRIT Individual Investigator Research Award (RP230382), and US Department of Defense Breakthrough Award (W81XWH-21-1-0114)."