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Eskin Lab Genetics and Genomics Software and Tools

Eskin Lab Genetics and Genomics Software and Tools. Has developed several tools for the analysis of genetics and genomics datasets. These tools and webservers which display the results of analysis with these tools are available to the scientific community. CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants. Next-generation Intersample Correlation Emended (...

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Eskin Lab Genetics and Genomics Software and Tools | genetics.cs.ucla.edu Reviews

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Eskin Lab Genetics and Genomics Software and Tools. Has developed several tools for the analysis of genetics and genomics datasets. These tools and webservers which display the results of analysis with these tools are available to the scientific community. CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants. Next-generation Intersample Correlation Emended (...

<META> KEYWORDS

1 overview

2 our group

3 human genetics

4 caviar

5 emmax

6 rarevariants

7 powerdesign

8 whap

9 nice

10 metasoft/forestpmplot

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overview,our group,human genetics,caviar,emmax,rarevariants,powerdesign,whap,nice,metasoft/forestpmplot,metasoft,grat,slip and slide,graphibd,tepaa,cnvem,harsh,pylmm,multitrans,gamma,mouse genetics,emma,emma study design,mpad,motif finding,mitra,smatch tr

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Eskin Lab Genetics and Genomics Software and Tools | genetics.cs.ucla.edu Reviews

https://genetics.cs.ucla.edu

Eskin Lab Genetics and Genomics Software and Tools. Has developed several tools for the analysis of genetics and genomics datasets. These tools and webservers which display the results of analysis with these tools are available to the scientific community. CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants. Next-generation Intersample Correlation Emended (...

INTERNAL PAGES

genetics.cs.ucla.edu

1

HARSH -- A Tool for Haplotype Inference using Reference and Sequencing Data

http://genetics.cs.ucla.edu/harsh

HAplotype inference using Reference and Sequencing tecHnology (HARSH) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method. HARSH was created by Wen-Yun Yang. Farhad Hormozdiari, Zhanyong Wang, Dan He, Bogdan Pasaniuc. Beta 2 version is posted! 2013-11-8) version 0.21, An IO bug fixed. 2013-10-28) Software beta 2 version posted online! Bug fixed and new features included. WY, FH., Z,...

2

SPA -- A Tool for Analysis of Spatial Structure in Genetic Data

http://genetics.cs.ucla.edu/spa

Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual's DNA. Accurately modeling ancestry is an important step in identifying genetic variation involved in disease. SPA was created by Wen-Yun Yang. For general questions, comments or suggestions about SPA, please email Eleazar Eskin (eeskin (AT) cs.ucla.edu). Version 1.10 was released on 2012-10-17, with support of personal genotype file from 23andMe. You can SUBSCRIBE to our mailing list.

3

GraphIBD

http://genetics.cs.ucla.edu/graphibd

Is a free, open-source IBD association testing software for genome-wide association study analysis. GraphIBD requires an IBD detection method such as Beagle FastIBD to run first. Then GraphIBD builds upon the IBD information to test if the IBD segments show association to the traits. This can be a powerful strategy to detect rare variant associations as shown in (Browning and Thompson, Genetics, 2012.). Provides the following methods:. GraphIBD version 0.1.0. Containing the followings,. Buhm Han, Eun Yon...

4

Next-generation Inter-sample Correlation Emended (NICE) eQTL mapping

http://genetics.cs.ucla.edu/nice_jemdoc

Download (.tar.gz). Next-generation Inter-sample Correlation Emended (NICE) eQTL (expression Quantitative Trait Loci) mapping and differential expression analysis. Is a statistical test for correcting for expression heterogeneity inherent in expression dataset due to confounding from unmodeled factors. NICE estimates inter-sample correlation structure using only the genes with confounding effects and incorporates it as signatures of the systematic confounding effects to correct for it. The full d...

5

METASOFT

http://genetics.cs.ucla.edu/meta_jemdoc

Correcting for population structure. Is a free, open-source meta-analysis software tool for genome-wide association study analysis, designed to perform a range of basic and advanced meta-analytic methods in an efficient manner. Provides the following methods:. Fixed Effects model (FE). Fixed effects model based on inverse-variance-weighted effect size. Random Effects model (RE). Conventional random effects model based on inverse-variance-weighted effect size (very conservative). Binary Effects model (BE).

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Eskin Lab Genetics and Genomics Software and Tools

Eskin Lab Genetics and Genomics Software and Tools. Has developed several tools for the analysis of genetics and genomics datasets. These tools and webservers which display the results of analysis with these tools are available to the scientific community. CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants. Next-generation Intersample Correlation Emended (...

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