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|Interface||Command line interface|
|Restrictions to use||None|
|License||GNU General Public License version 3.0|
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- person_outline Adam Siepel
Publication for LINSIGHT
Re analysis of public genetic data reveals a rare X chromosomal variant associated with type 2 diabetes
[…] 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
[…] 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
[…] 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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