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LINSIGHT specifications


Unique identifier OMICS_20662
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




No version available


  • person_outline Adam Siepel

Publication for LINSIGHT

LINSIGHT citations


Re analysis of public genetic data reveals a rare X chromosomal variant associated with type 2 diabetes

Nat Commun
PMCID: 5778074
PMID: 29358691
DOI: 10.1038/s41467-017-02380-9

[…] all possible substitutions of the human genome) metric for each 99% credible set variant, as it highly ranks causal variants within individual genome sequences (Supplementary Data ). We also used the LINSIGHT score to prioritize functional variants, which measures the probability of negative selection on noncoding sites by combining a generalized linear model for functional genomic data with a pro […]


Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression

PMCID: 5485531
PMID: 28635624
DOI: 10.3390/genes8060167

[…] ious 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 da […]


Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression

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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