KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited data | ||
| GM12878 Gro-seq | Core et al., 2014 | GSE60454 |
| GM12878 H3K27ac ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF180LKW |
| GM12878 H3K27me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF594HSG |
| GM12878 H3K36me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF662QFK |
| GM12878 H3K4me1 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF682WPF |
| GM12878 H3K4me2 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF828CQV |
| GM12878 H3K4me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF674QZB |
| GM12878 H3K4me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF818GNV |
| GM12878 H3K79me2 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF396JIR |
| GM12878 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF776OVW |
| GM12878 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF846MPX |
| GM12878 H4K20me1 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF831WYD |
| HCT-116 GRO-seq | Andrysik et al., 2017 | GSE86165 |
| IMR90 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF272ZUB |
| Kc167 H3K27ac ChIP-seq | Yang et al., 2013 | GSE36374 |
| Kc167 H3K27me3 ChIP-seq | Rowley et al., 2017 | GSE89244 |
| HCT-116 H3K27ac ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF225QAB |
| HCT-116 H3K27me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF030SYQ |
| HCT-116 H3K36me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF062CBC |
| HCT-116 H3K4me2 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF563OKQ |
| HCT-116 H3K4me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF057GFU |
| HCT-116 H3K4me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF859AQD |
| HCT-116 H3K79me2 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF127XQD |
| HCT-116 H3K9me2 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF854QMM |
| HCT-116 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF402WZH |
| HCT-116 H4K20me1 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF355TAA |
| HCT-116 H3K4me1 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF285DIL |
| IMR90 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF272ZUB |
| K562 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF834YLI |
| Kc167 H3K9me3 ChIP-seq | Rowley et al., 2017 | GSE89244 |
| Primary B cell H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF740QXN |
| H9 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF108MOZ |
| HCT-116 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF402WZH |
| Hepatocyte H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF354EPR |
| HepG2 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF881LOL |
| IMR90 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF272ZUB |
| K562 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF834YLI |
| Keratinocyte H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF242SAO |
| Liver H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF552IQT |
| Neutrophil H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF202TBY |
| Osteoblast H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF598YQV |
| PBMC1 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF319EBK |
| Stomach5 H3K9me3 ChIP-seq | ENCODE Project Consortium, 2012 | ENCFF995YEN |
| GM12878 Hi-C | Rao et al., 2014 | GSE63525 |
| HCT-116 Hi-C | Rao et al., 2017 | GSE104333 |
| Kc167 Hi-C | Cubeñas-Potts et al., 2017 | GSE80702 |
| Software and algorithms | ||
| seaborn | Seaborn, 2020 | https://seaborn.pydata.org/ |
| scikit-learn | Pedregosa et al., 2011 | https://scikit-learn.org/ |
| numpy | Oliphant, 2006 | https://numpy.org |
| scipy | Virtanen et al., 2020 | https://www.scipy.org/ |
| pandas | McKinney, 2010 | https://pandas.pydata.org |
| matplotlib | Hunter, 2007 | https://matplotlib.org |
| Juicebox | Durand et al., 2016 | https://www.aidenlab.org/juicebox/ |
| CIFSIM | This paper | https://github.com/5centmike/CIFSIM |