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Contents

  • MAGMA
  • FUMA
  • VEGAS
  • PASCAL
  • reviews

MAGMA

  • SHORT NAME: MAGMA
  • FULL NAME: Multi-marker Analysis of GenoMic Annotation
  • YEAR : 2015
  • DESCRIPTION:MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
  • URL: https://ctg.cncr.nl/software/magma
  • CITATION: de Leeuw, C. A., Mooij, J. M., Heskes, T., & Posthuma, D. (2015). MAGMA: generalized gene-set analysis of GWAS data. PLoS computational biology, 11(4), e1004219.

FUMA

  • FULL NAME:FUMA
  • SHORT NAME:FUMA
  • YEAR:2017
  • DESCRIPTION:FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results.
  • URL:https://fuma.ctglab.nl/
  • CITATION:Watanabe, Kyoko, et al. "Functional mapping and annotation of genetic associations with FUMA." Nature communications 8.1 (2017): 1-11.

PASCAL

  • FULL NAME:Pathway scoring algorithm
  • SHORT NAME:PASCAL
  • YEAR:2016
  • DESCRIPTION:Pascal (Pathway scoring algorithm) is an easy-to-use tool for gene scoring and pathway analysis from GWAS results.
  • URL:https://www2.unil.ch/cbg/index.php?title=Pascal
  • CITATION:Lamparter, David, et al. "Fast and rigorous computation of gene and pathway scores from SNP-based summary statistics." PLoS computational biology 12.1 (2016): e1004714.

VEGAS2

  • FULL NAME:Versatile Gene-based Association Study - 2 version 2
  • SHORT NAME:VEGAS2
  • YEAR:2015
  • DESCRIPTION:This is the VEGAS2 web platform. Here, user can perfome the gene-based and pathway-based analyses on GWAS summary data using VEGAS and VEGAS2Pathway approaches respectively. It is publically available for non-commercial use.
  • URL:https://vegas2.qimrberghofer.edu.au/
  • CITATION:Mishra, Aniket, and Stuart Macgregor. "VEGAS2: software for more flexible gene-based testing." Twin Research and Human Genetics 18.1 (2015): 86-91.

reviews

  • CITATION: White, Marquitta J., et al. "Strategies for pathway analysis using GWAS and WGS data." Current protocols in human genetics 100.1 (2019): e79.