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LINSIGHT specifications

Information


Unique identifier OMICS_20662
Name LINSIGHT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Adam Siepel <>

Publication for LINSIGHT

LINSIGHT in publications

 (3)
PMCID: 5778074
PMID: 29358691
DOI: 10.1038/s41467-017-02380-9

[…] loci, we annotated their corresponding credible sets using the variant effector predictor (vep) for coding variants (supplementary data ), and the combined annotation-dependent depletion (cadd) and linsight tools for non-coding variation (supplementary data  ). in addition, we tested the effect of all variants on expression across multiple tissues by interrogating gtex and rna-sequencing gene […]

PMCID: 5485531
PMID: 28635624
DOI: 10.3390/genes8060167

[…] annotation of genetic variants (dann) [], functional analysis through hidden markov models (fathmm) [], and linear inference of natural selection from interspersed genomically coherent elements (linsight) [] have been developed to predict functionality of variants outside the coding regions. these tools are based on supervised machine learning algorithms using a well-characterized training […]

PMCID: 5555460
PMID: 28600440
DOI: 10.1534/g3.117.043752

[…] a credible set to have similar statistical support (; ). inclusion of experimental evidence from epigenetic marks or signatures of evolutionary conservation into scores such as cadd (), cato (), and linsight () promises to improve resolution, as do methods such as rtc () and pics (), which prioritize variants based on the structure of ld at a locus. in general, these approaches assume parsimony, […]


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LINSIGHT institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Graduate Field of Computer Science, Cornell University, Ithaca, NY, USA
LINSIGHT funding source(s)
Supported by the US National Institutes of Health (NIH) grants GM102192 and HG008901.

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