Tag: Genetic association

Evian 2.1.0 – Evidential Analysis of Genetic Association Data

Evian 2.1.0

:: DESCRIPTION

Evian employs the Law of Likelihood, and uses the LR (likelihood ratio)rather than p-values to plan/design, analyze, interpret and replicate genetic association studies.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 Evian

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2010 Aug;18(8):933-41. doi: 10.1038/ejhg.2010.47. Epub 2010 Apr 28.
A pure likelihood approach to the analysis of genetic association data: an alternative to Bayesian and frequentist analysis.
Strug LJ1, Hodge SE, Chiang T, Pal DK, Corey PN, Rohde C.

RVS 20140305 – Genetic Association with NGS data

RVS 20140305

:: DESCRIPTION

The RVS (robust variance score) is a novel likelihood-based method for genetic association with NGS data from external control groups. RVS substitutes genotype calls by their expected values given observed sequence data and implements a robust variance estimate for the score statistic.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 RVS

:: MORE INFORMATION

Citation

Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic.
Derkach A, Chiang T, Gong J, Addis L, Dobbins S, Tomlinson I, Houlston R, Pal DK, Strug LJ.
Bioinformatics. 2014 Apr 14. pii: btu196.

LocusExplorer 0.7.2 – Visualisation of Human Genetic Association data and Biological Annotations

LocusExplorer 0.7.2

:: DESCRIPTION

LocusExplorer is a data visualisation and exploration tool for genetic association data.

::DEVELOPER

The Oncogenetics Team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 LocusExplorer

:: MORE INFORMATION

Citation

LocusExplorer: a user-friendly tool for integrated visualisation of human genetic association data and biological annotations.
Dadaev T, Leongamornlert DA, Saunders EJ, Eeles R, Kote-Jarai Z.
Bioinformatics. 2015 Nov 20. pii: btv690.

GAIN 0.2.0 – Genetic Association Interaction Network tool

GAIN 0.2.0

:: DESCRIPTION

GAIN is based on interaction information between three attributes; in this case, between two single nucleotide polymporphisms (SNPs) and a class or phenotype attribute. Interaction information is the gain in phenotype information obtained by considering SNP A and SNP B jointly beyond the phenotype information that would be gained by considering SNPs A and B independently.

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 GAIN

:: MORE INFORMATION

Citation

PLoS Genet. 2009 Mar;5(3):e1000432. doi: 10.1371/journal.pgen.1000432. Epub 2009 Mar 20.
Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis.
McKinney BA1, Crowe JE, Guo J, Tian D.

FAPI 0.1 – Fast and Accurate P-value Imputation for Genetic Association

FAPI 0.1

:: DESCRIPTION

FAPI is a powerful multi-thread Java-based application developed to infer p-values of untyped Single-nucleotide polymorphisms (SNPs) through p-values of SNPs in LD with the untyped one. With similar imputation accuracy to other genotype imputation tools (including IMPUTEand MACH), FAPI is superfast, without requiring phases of reference genotypes and any sample raw genotypes.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  FAPI

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2016 May;24(5):761-6. doi: 10.1038/ejhg.2015.190. Epub 2015 Aug 26.
FAPI: Fast and accurate P-value Imputation for genome-wide association study
Johnny S H Kwan, Miao-Xin Li, Jia-En Deng , Pak C Sham

MEAGA 1.2 – Minimum distance-based Enrichment Analysis for Genetic Association

MEAGA 1.2

:: DESCRIPTION

MEAGA performs functional/pathway enrichment test while integrating network information from biological interactome (e.g. protein-protein interaction network) using graphical algorithm techniques.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MEAGA

:: MORE INFORMATION

Citation

Graphical algorithm for integration of genetic and biological data: Proof of principle using psoriasis as a model.
Tsoi LC, Elder JT, Abecasis GR.
Bioinformatics. 2014 Dec 4. pii: btu799.

metagen – Meta-analysis of Genetic association Studies

metagen

:: DESCRIPTION

metagen performs fixed-, and random-effects meta-analysis of genetic association case-control studies using Individual Patient Data (IPD). metagen performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables. By default, metagen performs tests for the overall heterogeneity of the genotypes effects, for the heterogeneity of the assumed genetic model of inheritance as well as for the between-studies heterogeneity of the genetic model.

::DEVELOPER

Computational Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Stata

:: DOWNLOAD

 metagen

:: MORE INFORMATION

Citation

Bagos PG, Nikolopoulos GK.
A method for meta-analysis of case-control genetic association studies using logistic regression. 2007,
Statistical Applications in Genetics and Molecular Biology, 6(1): Article 17

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