MeRP 1.0 – Mendelian Randomization analysis

MeRP 1.0

:: DESCRIPTION

MeRP is a free, open-source tool designed to streamline and automate large-scale Mendelian Randomization analysis.

::DEVELOPER

Peter Yin, Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MeRP

:: MORE INFORMATION

Citation

MeRP: a high-throughput pipeline for Mendelian Randomization Analysis.
Yin P, Voight BF.
Bioinformatics. 2014 Nov 10. pii: btu742

MR-JTI v1 – Joint-tissue Transcriptome-wide Association and Mendelian Randomization analysis

MR-JTI v1

:: DESCRIPTION

MR-JTI is a joint-tissue imputation (JTI) approach and a Mendelian randomization framework for causal inference.

::DEVELOPER

Gamazon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

MR-JTI

 :: MORE INFORMATION

Citation

Zhou D, Jiang Y, Zhong X, Cox NJ, Liu C, Gamazon ER.
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis.
Nat Genet. 2020 Nov;52(11):1239-1246. doi: 10.1038/s41588-020-0706-2. Epub 2020 Oct 5. PMID: 33020666; PMCID: PMC7606598.

PARIS 1.1.3 – Pathway Analysis by Randomization Incorporating Structure

PARIS 1.1.3

:: DESCRIPTION

PARIS is independent of association analysis method and is thus applicable to GWAS datasets of all study designs.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PARIS

:: MORE INFORMATION

Citation

Hum Genet. 2011 May;129(5):563-71. doi: 10.1007/s00439-011-0956-2.
Genetic analysis of biological pathway data through genomic randomization.
Yaspan BL, Bush WS, Torstenson ES, Ma D, Pericak-Vance MA, Ritchie MD, Sutcliffe JS, Haines JL.

JMassBalance 20130207 – Mass-balanced Randomization and Analysis of Metabolic Networks

JMassBalance 20130207

:: DESCRIPTION

JMassBalance is a tool for mass-balanced randomization and analysis of metabolic networks. The tool allows efficient generation of large sets of randomized networks under the physical constraint of mass balance. In addition, various structural properties of the original and randomized networks can be calculated, facilitating the identification of the salient properties of metabolic networks with a biologically meaningful null model.

::DEVELOPER

Systems biology and Mathematical Modelling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 JMassBalance

:: MORE INFORMATION

Citation

Georg Basler and Zoran Nikoloski (2011):
JMassBalance: mass-balanced randomization and analysis of metabolic networks.
Bioinformatics, 27(19):2761-2762. doi:10.1093/bioinformatics/btr448