geQTL – Unraveling Group and individual Associations in eQTL Mapping

geQTL

:: DESCRIPTION

geQTL is a sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits.

::DEVELOPER

Wei Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / MatLab

:: DOWNLOAD

 geQTL

:: MORE INFORMATION

Citation

Sparse regression models for unraveling group and individual associations in eQTL mapping.
Cheng W, Shi Y, Zhang X, Wang W.
BMC Bioinformatics. 2016 Mar 22;17(1):136. doi: 10.1186/s12859-016-0986-9.

GenAMap 3.3 – Visual Analytics Software Platform for eQTL and GWAS Analysis

GenAMap 3.3

:: DESCRIPTION

GenAMap is a visual analytics system for structured association mapping. The software brings the power of structured association mapping to a usable, intuitive interface.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

GenAMap

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GenAMap

:: MORE INFORMATION

Citation

Finding genome-transcriptome-phenome association with structured association mapping and visualization in GenAMap.
Curtis RE, Yin J, Kinnaird P, Xing EP.
Pac Symp Biocomput. 2012:327-38.

EPSILON – eQTL Prioritization using Similarity Measures derived from Local Interaction Networks

EPSILON

:: DESCRIPTION

EPSILON is an extendable framework for eQTL prioritization, which mitigates the effect of highly connected genes and unreliable interactions by constructing a local network before a network-based similarity measure is applied to select the true causal gene.

::DEVELOPER

Lieven P.C. Verbeke lieven.verbeke@intec.ugent.be or jan.fostier@intec.ugent.be

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Matlab/C++

:: DOWNLOAD

  EPSILON

:: MORE INFORMATION

Citation:

Lieven P. C. Verbeke; Lore Cloots; Piet Demeester; Jan Fostier; Kathleen Marchal
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks
Bioinformatics (2013) 29 (10): 1308-1316.

GGD-Lasso – Graph-regularized dual Lasso for robust eQTL mapping

GGD-Lasso

:: DESCRIPTION

GGD-Lasso (Graph-regularized Dual Lasso) is a robust approach for eQTL mapping.

::DEVELOPER

Wei Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler / MatLab

:: DOWNLOAD

 GGD-Lasso

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i139-i148. doi: 10.1093/bioinformatics/btu293.
Graph-regularized dual Lasso for robust eQTL mapping.
Cheng W, Zhang X, Guo Z, Shi Y, Wang W.

PANAMA 0.58 – Account for Confounding Factors in eQTL Studies

PANAMA 0.58

:: DESCRIPTION

PANAMA (Probabilistic ANAlysis of genoMic dAta) is a novel probabilistic model to account for confounding factors within an eQTL analysis.

::DEVELOPER

Stegle group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Python
  • Numpy and Scipy

:: DOWNLOAD

 PANAMA

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2012 Jan;8(1):e1002330. doi: 10.1371/journal.pcbi.1002330. Epub 2012 Jan 5.
Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND.

eMap 1.2 – eQTL Analysis

eMap 1.2

:: DESCRIPTION

eMap is a software for eQTL computation, visiualization, eQTL module, integrated studies of complex trait, gene epression and genetic markers, etc.

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

  eMap

:: MORE INFORMATION

eQTL.TF 1.1 – eQTL and Transcription Regulation.

eQTL.TF 1.1

:: DESCRIPTION

eQTL.TF is a software for gene expression quantitative trait loci analysis. The software based on gene expression data and marker data, map eQTL and carry out subsequent analysis

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 eQTL.TF

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 1;23(17):2290-7. Epub 2007 Jun 28.
Detection of eQTL modules mediated by activity levels of transcription factors.
Sun W, Yu T, Li KC.

seeQTL – A Searchable Human eQTL Browser and database

seeQTL

:: DESCRIPTION

seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots.

::DEVELOPER

Department of Biostatistics, Computer Sciences and Genetics, University of North Carolina at Chapel Hill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

K. Xia, A.A. Shabalin, S. Huang, V. Madar, Y.H. Zhou, W. Wang, F. Zou, W. Sun, P.F. Sullivan, and F.A. Wright
seeQTL: A searchable database for human eQTLs
Bioinformatics (2012) 28(3): 451-452

eQTLexplorer 6.0 – eQTL Visualization tool

eQTLexplorer 6.0

:: DESCRIPTION

eQTLexplorer is an eqtl visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments.

::DEVELOPER

Michael Mueller, Jon Mangion

:: SCREENSHOTS

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 eQTLexplorer

:: MORE INFORMATION

Citation

Mueller M et al. (2006)
eQTLexplorer: integrated mining of genetical genomics experiments.
Bioinformatics, 22: 509-11