iCTNet 0.1 – Analyze Integrative Complex Traits Networks

iCTNet 0.1

:: DESCRIPTION

iCTNet (integrated Complex Traits Network) is a large-scale network, assembling human disease-gene association, tissue-gene association, disease-tissue associations, protein-DNA interactions, protein-protein interactions and drug-target information.

::DEVELOPER

iCTNet team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 iCTNet

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Sep 26;12:380. doi: 10.1186/1471-2105-12-380.
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.
Wang L1, Khankhanian P, Baranzini SE, Mousavi P.

traseR 1.14.0 – GWAS Trait-associated SNP Enrichment Analyses in Genomic Intervals

traseR 1.14.0

:: DESCRIPTION

traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.

::DEVELOPER

li chen<li.chen at emory.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • R/ BioConductor

:: DOWNLOAD

 traseR

:: MORE INFORMATION

Citation:

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
Chen L, Qin Z.
Bioinformatics. 2015 Dec 18. pii: btv741.

aSPU 1.39 – Adaptive Gene- and Pathway-Trait Association Testing with GWAS

aSPU 1.39

:: DESCRIPTION

aSPU is an R package for adaptive sum of powered score test(ASPU) in genetic association studies.

::DEVELOPER

Il-Youp Kwak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • R

:: DOWNLOAD

 aSPU

:: MORE INFORMATION

Citation

Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics.
Kwak IY, Pan W.
Bioinformatics. 2015 Dec 10. pii: btv719.

BaTS 1.0 – Measure and Test Phylogeny Trait Associations

BaTS 1.0

:: DESCRIPTION

BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

BaTS

:: MORE INFORMATION

Citation:

Parker J, Rambaut A, Pybus OG. 2008.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Infection, Genetics and Evolution 8:239-46

Phyto-PhyloPars – Phylogenetic approach to the Estimation of Phytoplankton Traits

Phyto-PhyloPars

:: DESCRIPTION

Phyto-PhyloPars web server takes an evolutionary perspective to the variability across phytoplankton taxa in order to estimate the size, maximum growth rate, phosphate affinity and susceptibility to predation of any phytoplankton taxon, based on over one thousand observations on freshwater species.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bruggeman, J. (2011)
A phylogenetic approach to the estimation of phytoplankton traits.
Journal of Phycology 47(1): 52-65.

MTDFREML – Multiple-Trait Derivtive-Free Restricted Maximum Likelihood

MTDFREML

:: DESCRIPTION

MTDFREML is aset of programs for estimation of genetic (co)variances using multiple-trait derivative-free restricted maximum likelihood

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortron

:: DOWNLOAD

 MTDFREML

:: MORE INFORMATION

Citation

J Anim Sci. 1996 Nov;74(11):2586-97.
Multiple-trait Gibbs sampler for animal models: flexible programs for Bayesian and likelihood-based (co)variance component inference.
Van Tassell CP1, Van Vleck LD.

TM 20110802 – Multiple Trait Estimation of Variance Components

TM 20110802

:: DESCRIPTION

TM (Threshold Model) is a (Fortran90) software for multiple trait estimation of variance components, breeding values and fixed effects in threshold, linear and censored linear models in animal breeding.  As of August, 2011 it has been modified to accept random seeds on input, and also to include user-defined covariance matrices among individuals (for instance, genomic relationship matrices).

::DEVELOPER

Andrés Legarra , andres dot legarra at toulouse point inra punto fr

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Fortran90

:: DOWNLOAD

 TM

:: MORE INFORMATION

Epistasis-HS – Assess the Degree of Epistasis for a given Trait

Epistasis-HS

:: DESCRIPTION

Epistasis-HS allow you to assess the degree of epistasis for a given trait between a pair of maternal or paternal half-sib families. You are only able to use this program to calculate epistasis between a pair of half-sib families.  If your mating structure involves multiple half-sib families (i.e., k > 2) you will need to recalculate estimates among all the possible pairwise half-sib groupings  (i.e., k*(k-1) / 2 pairwise combinations).

::DEVELOPER

Roy G. Danzmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Epistasis-HS

:: MORE INFORMATION

MapMaker 3 – Genetic Linkage Analysis & Mapping Genes Complex Traits

MapMaker 3

:: DESCRIPTION

MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

MAPMAKER/EXP is a linkage analysis package designed to help construct primary linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co-dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program.

MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL).

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

MapMaker

:: MORE INFORMATION

Citation

Please use Lander et al. 1987 for MAPMAKER/EXP, and Paterson et al. 1988 for
MAPMAKER/QTL. Please also cite:

S. Lincoln, M. Daly, and E. Lander: Constructing Genetic Maps with MAPMAKER/EXP
3.0. (1992) Whitehead Institute Technical Report. 3rd edition.

S. Lincoln, M. Daly, and E. Lander: Mapping Genes Controlling Quantitative
Traits with MAPMAKER/QTL 1.1. (1992) Whitehead Institute Technical Report. 2nd
edition.