RVIS – Residual Variation Intolerance Score

RVIS

:: DESCRIPTION

RVIS is a gene-based score intended to help in the interpretation of human sequence data.

::DEVELOPER

RVIS  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS Genet. 2013;9(8):e1003709. doi: 10.1371/journal.pgen.1003709. Epub 2013 Aug 22.
Genic intolerance to functional variation and the interpretation of personal genomes.
Petrovski S1, Wang Q, Heinzen EL, Allen AS, Goldstein DB.

PRSice v1.21 – Polygenic Risk Score software

PRSice v1.21

:: DESCRIPTION

PRSice is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores.

::DEVELOPER

PRSice team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • R

:: DOWNLOAD

 PRSice

:: MORE INFORMATION

Citation

PRSice: Polygenic Risk Score software.
Euesden J, Lewis CM, O’Reilly PF.
Bioinformatics. 2014 Dec 29. pii: btu848.

MOST 1.0 – Multivariate Outcome Score Test

MOST 1.0

:: DESCRIPTION

MOST (Multivariate Outcome Score Test) is able to analyze all the traits jointly. The framework is flexible in that it can handle both continuous and binary traits, or a mixture of them. In addition, it can accommodate family data, can adjust for covariates (such as ancestry variables, age, gender, etc.), and can be combined efficiently across studies with different designs. Furthermore, it has a built-in Monte Carlo procedure that can determine the genome-wide significance by taking into account the LD information among all the SNPs. Tur framework establishes a flexible platform for the analysis of multivariate-outcome association study, and provides a powerful tool for uncovering pleiotropic genetic variants.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

MOST

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Dec;37(8):759-67. doi: 10.1002/gepi.21759. Epub 2013 Nov 5.
A general framework for association tests with multivariate traits in large-scale genomics studies.
He Q1, Avery CL, Lin DY.

iHS_calc 1.0.1 – Calculate the Integrated Hapotype Score

iHS_calc 1.0.1

:: DESCRIPTION

iHS_calc is designed to calculate the integrated Hapotype Score (iHS).

::DEVELOPER

Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  iHS_calc

:: MORE INFORMATION

Citation:

PLoS Biol. 2006 Mar;4(3):e72. Epub 2006 Mar 7.
A map of recent positive selection in the human genome.
Voight BF1, Kudaravalli S, Wen X, Pritchard JK.

RHScorer 2.1 – Score Gels

RHScorer 2.1

:: DESCRIPTION

RHScorer is used to score gels. The software consists of client applet and a server.The server is used to maintain the Gel Images and scores. The applet is used to score the gels.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 RHScorer

:: MORE INFORMATION

GA2GAQ – GO Annotation Quality(GAQ) Score

GA2GAQ

:: DESCRIPTION

GA2GAQ allows user to quantitatively assess GO annotation of a set of gene products. The GAQ score includes breadth of GO annotation, level of detail for annotation and type of evidence used to make the annotation. The output is a summary of total GAQ scores for each gene product, the number of gene products annotated and the average (mean) GAQ score of the whole set.

:: DEVELOPER

AgBase, Department of Basic Science,College of Veterinary Medicine, Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Perl

:: DOWNLOAD

 GA2GAQ

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Feb;36(2):e12. doi: 10.1093/nar/gkm1167.
Gene Ontology annotation quality analysis in model eukaryotes.
Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC.

nuScore – DNA Deformation Energy and Nucleosome-positioning Score Calculator

nuScore

:: DESCRIPTION

nuScore allows estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. The algorithm is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface

::DEVELOPER

Computational Genomics (PI: Peter J Park)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.
nuScore: a web-interface for nucleosome positioning predictions.
Bioinformatics. 2008. 24:1456-1458.

LSim 1.0.0 – Superposes Macromolecular Electron Densities and Computes Structural Similarity Score

LSim 1.0.0

:: DESCRIPTION

LSim superposes macromolecular electron densities and computes a structural similarity score. LSim computations scale linearly with the size of the molecules being compared.

::DEVELOPER

Pere Constans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LSim

:: MORE INFORMATION

Citation

Constans, P.
Linear Scaling Approaches to Quantum Macromolecular Similarity: Evaluating the Similarity Function.
J. Comput. Chem. 23, 1305-1313, 2002

NePhe 1.0 – Network RNAi Phenotype Score

NePhe 1.0

:: DESCRIPTION

NePhe (Network RNAi Phenotype) is intended to implement a network-based integrative approach to prioritize reliable hits in genome-wide screens

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NePhe

:: MORE INFORMATION

Citation

Wang L, Tu Z, Sun FZ (2009)
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.
BMC Genomics 10:220.

ClusterJudge – Score the Results from any Clustering Algorithm

ClusterJudge

:: DESCRIPTION

ClusterJudge scores the results from any clustering algorithm, using existing annotation, so you can see which one best groups genes by function.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ClusterJudge

:: MORE INFORMATION

Citation

Gibbons, F.D. and Roth F.P., (2002)
Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation.
Genome Research, vol. 12, pp1574-1581.