JAG 1.1 – Gene-set Analysis in GWAS Datasets

JAG 1.1

:: DESCRIPTION

JAG (Joint Association of Genetic Variants) is a free open source tool to run gene-set analysis in GWAS data. It uses raw data as input and includes bot self-contained and competitive tests.

::DEVELOPER

CTG (Complex Traits Genetics) Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

 JAG

:: MORE INFORMATION

Piano 2.8.0 – An R/Bioconductor package for Gene Set Analysis

Piano 2.8.0

:: DESCRIPTION

Piano is an R/Bioconductor package that is used for running gene set analysis and is also capable of performing basic microarray analysis.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Piano

:: MORE INFORMATION

Citation

Väremo, L., Nielsen, J. and Nookaew, I. (2013)
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods.
Nucleic Acids Research. 41 (8), 4378-4391. DOI:10.1093/nar/gkt111

Kiwi 0.3.6 – Visualization of Network Topology and Gene-set Analysis

Kiwi 0.3.6

:: DESCRIPTION

The Kiwi module combines geneset analyses with biological networks to visualize the interactions between genesets that are significant in a given biological system.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Kiwi

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 11;15:408. doi: 10.1186/s12859-014-0408-9.
Kiwi: a tool for integration and visualization of network topology and gene-set analysis.
Väremo L, Gatto F, Nielsen J