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. 2023 Jun 13;5(3):zcad028. doi: 10.1093/narcan/zcad028

Table 1.

Analytical tools for Hi-C analysis

Software Version Reference
bwa 0.7.17-r1188 (35)
pairtools v0.3.0 (36)
cooltools v0.4.0 (36)
TopDom v0.10.1 (37)
HiCExplorer v3.7 (40)
neoloopfinder 0.2.4.post2 (39)
R v4.0.0 https://www.r-project.org/
juicebox 2.2.2 (41)
diffHic v1.22.0 (38)
hicbreakfinder NA https://github.com/dixonlab/hic_breakfinder
ENCODE ChIP-seq v2.1.2 (42)
deeptools v3.3.1 (43)
HOMER v4.11.1 (34)
HiGlass v1.11.7 (44)