Fit-Hi-C statistics

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Fit-Hi-C specifications

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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 in publications

 (18)
PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] 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 […]

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

[…] and were normalized using the ice method to correct for experimental and technical biases (fig. , supplementary data , and supplementary data ). in addition, we identified significant contacts using fit-hi-c, which controls for the propensity of adjacent loci to have more contacts and calculates a p-value reflecting the probability that the number of contacts in that bin is larger than expected […]

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

[…] reflect all biology, the regions containing rs28665337 and rs17481869 show significant chromatin looping interactions with the promotor regions of myc in es cells and gtdc1 in gm12878, respectively (fit-hi-c test, supplementary figs.  )., a relationship between variation within the major histocompatibility complex (mhc) region and risk of all has long been speculated–. however, most studies […]

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 […]

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

[…] 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 […]


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

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