INRICH 1.1 – Interval-based Enrichment Analysis Tool for Genome Wide Association Studies

INRICH 1.1

:: DESCRIPTION

INRICH is a pathway analysis tool for genome wide association studies, designed for detecting enriched association signals of LD-independent genomic regions within biologically relevant gene sets.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

INRICH

:: REQUIREMENTS

  • Linux/Windows/ MacOsX

:: DOWNLOAD

 INRICH

:: MORE INFORMATION

Citation

INRICH: interval-based enrichment analysis for genome-wide association studies.
Lee PH, O’Dushlaine C, Thomas B, Purcell SM.
Bioinformatics. 2012 Jul 1;28(13):1797-9. doi: 10.1093/bioinformatics/bts191.

easyGWAS – Platform for performing Genome-wide Association Studies

easyGWAS

:: DESCRIPTION

easyGWAS is designed to be a central resource for the genetics community that frees the user from the tedious tasks of implementing statistical software and managing data and computing resources and that serves the community at large through easy data access, validation and reproduction of GWAS findings.

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Dominik Grimm, Bastian Greshake, Stefan Kleeberger, Christoph Lippert, Oliver Stegle, Bernhard Sch?kopf, Detlef Weigel and Karsten Borgwardt:
easyGWAS: An integrated interspecies platform for performing genome-wide association studies,
arXiv preprint arXiv:1212.4788, 2012

PBOOST – Parallel Permutation Tests in Genome-wide Association Studies

PBOOST

:: DESCRIPTION

PBOOST is a GPU based tool for parallel permutation tests in genome-wide association studies.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

PBOOST

:: REQUIREMENTS

:: DOWNLOAD

  PBOOST 

:: MORE INFORMATION

Citation:

PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.
Yang G, Jiang W, Yang Q, Yu W.
Bioinformatics. 2014 Dec 21. pii: btu840.

gowinda 1.12 – Gene Ontology Term Enrichment for Genome Wide Association Studies

gowinda 1.12

:: DESCRIPTION

Gowinda is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Python

:: DOWNLOAD

 gowinda

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 1;28(15):2084-5. doi: 10.1093/bioinformatics/bts315. Epub 2012 May 26.
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.
Kofler R1, Schlötterer C.

PEPIS 1.0 – Estimating EPIStatic effect in Linkage Mapping and Genome-Wide Association Studies

PEPIS 1.0

:: DESCRIPTION

PEPIS is a pipeline that is dedicatedly developed for Polygenic, specifically, Epistatic QTL mapping.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PEPIS

:: MORE INFORMATION

Citation

PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.
Zhang W, Dai X, Wang Q, Xu S, Zhao PX.
PLoS Comput Biol. 2016 May 25;12(5):e1004925. doi: 10.1371/journal.pcbi.1004925.

GWAtoolbox 2.2.4-7 – Quality Control and Handling of Genome-wide Association Studies Meta-analysis data

GWAtoolbox 2.2.4-7

:: DESCRIPTION

GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS).

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R package

:: DOWNLOAD

 GWAtoolbox

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):444-5. doi: 10.1093/bioinformatics/btr679.
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data.
Fuchsberger C, Taliun D, Pramstaller PP, Pattaro C; CKDGen consortium.

FINEMAP 1.0 – Efficient Variable Selection using summary data from Genome-wide Association Studies

FINEMAP 1.0

:: DESCRIPTION

FINEMAP is a computationally efficient program for fine-mapping in genomic regions associated with complex diseases and traits via a shotgun stochastic search algorithm (Hans et al., 2007).

::DEVELOPER

 

Christian Benner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 FINEMAP

:: MORE INFORMATION

Citation

FINEMAP: Efficient variable selection using summary data from genome-wide association studies.
Benner C, Spencer CC, Havulinna AS, Salomaa V, Ripatti S, Pirinen M.
Bioinformatics. 2016 Jan 14. pii: btw018.

LDetect – Automated Analysis of Multiple Genome-wide Association Studies

LDetect

:: DESCRIPTION

LDetect is a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome.

::DEVELOPER

LDetect team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 LDetect

:: MORE INFORMATION

Citation

Approximately independent linkage disequilibrium blocks in human populations.
Berisa T, Pickrell JK.
Bioinformatics. 2015 Sep 22. pii: btv546

repfdr 1.1-3 – Replicability Analysis for Multiple Studies of High Dimension

repfdr 1.1-3

:: DESCRIPTION

repfdr is a tool for replicability analysis for genome-wide association studies.

::DEVELOPER

Ruth Heller

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 repfdr

:: MORE INFORMATION

Citation:

repfdr: A tool for replicability analysis for genome-wide association studies.
Heller R, Yaacoby S, Yekutieli D.
Bioinformatics. 2014 Jul 9. pii: btu434.

MultiMeta 0.1 – Meta-analysis of Multivariate Genome Wide Association Studies

MultiMeta 0.1

:: DESCRIPTION

The R package MultiMeta provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting.

::DEVELOPER

Dragana Vuckovic <dragana.vuckovic at burlo.trieste.it>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 MultiMeta

:: MORE INFORMATION

Citation:

MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.
Vuckovic D, Gasparini P, Soranzo N, Iotchkova V.
Bioinformatics. 2015 Apr 22. pii: btv222