HiChIP statistics

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HiChIP specifications


Unique identifier OMICS_05377
Name HiChIP
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R, Shell (Bash)
Computer skills Advanced
Stability Stable
Cython, Numpy, FastQC, BWA, MACS, SICER, IGVTools, Samtools, MEME, CEAS, Picard, BEDTools
Source code URL https://s3-us-west-2.amazonaws.com/mayo-bic-tools/chipseq/chipseq_release.tgz
Maintained Yes


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Publication for HiChIP

HiChIP in publications

PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] multiplex system (nugen). the chip-seq libraries were sequenced to 51 base pairs from both ends using the illumina hiseq 2000 in the mayo clinic medical genomics core. data were analyzed using the hichip pipeline. briefly, paired-end reads were mapped by bwa and pairs with one or both ends uniquely mapped were retained. h3k4me3, h3k4me1, and h3k27ac peaks were called using the macs2 software […]

PMCID: 5924553
PMID: 29659513
DOI: 10.3390/genes9040211

[…] have coordinated activities, resulting in coordinated gene expression in the same tads [,,]., with the development of super-resolution hi-c and other 3c-based methods such as chia-pet, capture hi-c, hichip, and plac-seq, specific long-range interactions between functional loci, or chromatin looping, can be detected [,,,,]. chromatin looping interactions are insulated by tad boundaries; hence, […]

PMCID: 5929158
PMID: 29641996
DOI: 10.1016/j.celrep.2018.03.056

[…] but the mechanisms responsible for this specific interaction are unclear (). to gain insights into the potential role of dna loop structures in gene control at the myc locus, we generated cohesin hichip data for hct-116 cells and collected published dna interaction data for three other cancer cell types for comparison (; and ) (; ). among the dna loop structures observed in these datasets, […]

PMCID: 5827651
PMID: 29497530
DOI: 10.1002/cti2.1011

[…] regulation. these assays directly identify genomic loci that are in sufficiently close proximity in living cells to be cross‐linked. several versions of 3c such as 4cseq, chia‐pet, 5c hichip and hi‐c allow for mapping of chromatin interactions on a whole genome level. recently, to improve the resolution and sensitivity of hi‐c assays, in situ protocols have been developed. […]

PMCID: 5768180
PMID: 29367853
DOI: 10.3389/fimmu.2017.01938

[…] nyu genome center for single end sequencing on illumina hiseq to a depth of 20 million reads in the case of primary b cells and 40 million reads for ramos b cells., chip-seq data was processed by hichip (). reads were mapped to the hg19 human reference sequences using bwa at default parameters (). peaks were called using the macs2 algorithm at the following parameters (p = 0.0001, m = 10.30) […]

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HiChIP institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA; Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
HiChIP funding source(s)
Supported by the Center for Individualized Medicine, Mayo Clinic, Rochester, MN.

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