Table 1.

Representative computational packages for analyses of chromatin capture experiments. Each package is implemented in the R language for statistical computing and the focus of the data type and function of the analytical approache alongside the relevant publications are indicated.

Package	Focus	Function	Publication
sevenC	CTCF ChIP-Seq	Predicts chromatin loops from CTCF ChIP-Seq data
diffloop	ChIA-PET and RNA-Seq	Identify differential chromatin topology between cell conditions and annotate with gene expression	(165)
R3Cseq	3C	Identify genomic loops between two fixed points	(166)
CHiCAGO	Capture-Hi-C	Analyses of HiC data that are enriched for genomic features of interest	(167)
HiTC	Hi-C	Normalization and visualization of Hi-C data, TAD detection	(168)
multiHiCcompare	Hi-C	Normalization and visualization of Hi-C data, TAD detection	(144)
HiCRep HiCseg	Hi-C	Assess reproducibility in Hi-C data, and ormalization and visualization of Hi-C data, TAD detection	(169)
TopDom	Hi-C	Normalization and visualization of Hi-C data, TAD detection	(148)