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Fit-Hi-C specifications


Unique identifier OMICS_03489
Name Fit-Hi-C
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for Fit-Hi-C

Fit-Hi-C citations


Thirty loci identified for heart rate response to exercise and recovery implicate autonomic nervous system

Nat Commun
PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] enitor stem cells, hippocampus and cortex which tissues and cell types are considered relevant for regulating heart rate. Hi–C data is corrected for genomic biases and distance using the Hi–C Pro and Fit-Hi-C pipelines according to Schmitt et al. (40 kb resolution—correction applied to interactions with 50 kb-5 Mb span). We find the most significant promoter interactions for all potential regulato […]


Changes in genome organization of parasite specific gene families during the Plasmodium transmission stages

Nat Commun
PMCID: 5954139
PMID: 29765020
DOI: 10.1038/s41467-018-04295-5

[…] tures when compared to the optimization-based approach we used previously. To identify significant contacts, we modeled the effect of genomic distance on contact count probability with a spline using fit-hi-c. Because of the possibility of differing statistical power between datasets, we report both the number of significant contacts above a given threshold, as well as the percent of significant c […]


Genome wide association study identifies susceptibility loci for B cell childhood acute lymphoblastic leukemia

Nat Commun
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] ively. Plotted topologically associating domains boundaries were obtained from the insulating score method at 40 kb bin resolution. We searched for significant interactions (P-values generated using “Fit-Hi-C”) between bins overlapping the currently identified ALL risk loci with target genes (e.g., “virtual 4C”). […]


Dissecting super enhancer hierarchy based on chromatin interactions

Nat Commun
PMCID: 5838163
PMID: 29507293
DOI: 10.1038/s41467-018-03279-9

[…] in each cell type were detected as previously described. Briefly, the raw interaction matrix was normalized by using the ICE algorithm, as implemented in the Hi-Corrector package, to remove biases,. Fit-Hi-C was used to identify statistically significant intra-chromosomal interactions, using the parameter setting ‘-U = 2000000, -L = 10000’ along with the threshold of FDR = 0.01. The interaction f […]


TADs are 3D structural units of higher order chromosome organization in Drosophila

Sci Adv
PMCID: 5829972
PMID: 29503869
DOI: 10.1126/sciadv.aar8082

[…] ersists for configurations where the intra-TAD distance is higher than the inter-TAD distance (≤10% overlap in 85% of the inferred configurations; ). Therefore, polymer modeling using parameters that fit Hi-C maps supports the frequent folding of the two TADs into well-separated nanocompartments. The fraction of intra-TAD distances larger than the inter-TADs counterparts is thus explained by the d […]


Enhancing Hi C data resolution with deep convolutional neural network HiCPlus

Nat Commun
PMCID: 5821732
PMID: 29467363
DOI: 10.1038/s41467-018-03113-2

[…] solution Hi-C interaction matrix, we investigated whether these enhanced high-resolution matrices can facilitate the identification of meaningful chromatin interactions. For this purpose, we used the Fit-Hi-C software, which can adjust random polymer looping effect and estimate statistical confidence of intra-chromosomal interactions. We applied Fit-Hi-C to the real high-resolution, 1/16 down-samp […]


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Fit-Hi-C institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA

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