CHiCAGO specifications


Unique identifier OMICS_10160
Alternative name Capture HiC Analysis of Genomic Organisation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Mikhail Spivakov

Publication for Capture HiC Analysis of Genomic Organisation

CHiCAGO citations


Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation

Nucleic Acids Res
PMCID: 5622376
PMID: 28973456
DOI: 10.1093/nar/gkx659

[…] pes from the IHEC project () to evaluate the ability of our states to predict chromatin interactions. We used the inferred chromatin states within both bait and target regions to predict the CHiCAGO (Capture HiC Analysis of Genomic Organisation) interaction scores (). As we have shown in the FANTOM5 data, the state co-occurrence between two interacting regions was not random. This is also true in […]


Capture Hi C identifies a novel causal gene, IL20RA, in the pan autoimmune genetic susceptibility region 6q23

Genome Biol
PMCID: 5088679
PMID: 27799070
DOI: 10.1186/s13059-016-1078-x

[…] terrogated regions, compared to adjacent non-interacting regions (Fig. ).Fig. 2 To validate our analysis method, we reanalysed our CHi-C data using a recently developed analytical algorithm, CHiCAGO (Capture HiC Analysis of Genomic Organisation ( The pattern of chromatin loops obtained when we applied CHiCAGO was more complex, although it confirm […]

CHiCAGO institution(s)
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK; Bioinformatics Group, Babraham Institute, Cambridge, UK; UCL Genetics Institute, London, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK; Department of Medical and Molecular Genetics, King’s College, London, UK
CHiCAGO funding source(s)
The Biotechnology and Biological Sciences Research Council; the Medical Research Council of the UK; the European Molecular Biology Laboratory

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