VEGAS2Pathway specifications

Unique identifier:
OMICS_15245
Restrictions to use:
None
Input format:
GWAS
Programming languages:
Perl, R
Version:
2.0
Maintained:
Yes
Interface:
Web user interface
Input data:
Association results as a text file with two columns.
Output data:
The gene-based output is a plain-text file with the columns: Chromosome, Gene, Number of SNPs, Number of simulations, Start position, Stop position, Gene-based test statistic, P-value, Top-SNP, Top-SNP pvalue. The pathway-based output is also a plain-text file with the columns: GO_ID, Description, Pathway length, Pathway length after first cut, Pathwal length after second cut, Final pathway length, Combined p-value, Emipirical p-value, Genelist.
Computer skills:
Basic
Stability:
Stable

VEGAS2Pathway specifications

Unique identifier:
OMICS_15245
Interface:
Command line interface
Input data:
Association results as a text file with two columns.
Output data:
The gene-based output is a plain-text file with the columns: Chromosome, Gene, Number of SNPs, Number of simulations, Start position, Stop position, Gene-based test statistic, P-value, Top-SNP, Top-SNP pvalue. The pathway-based output is also a plain-text file with the columns: GO_ID, Description, Pathway length, Pathway length after first cut, Pathwal length after second cut, Final pathway length, Combined p-value, Emipirical p-value, Genelist.
Programming languages:
Perl, R
Stability:
Beta
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Input format:
GWAS
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Requirements:
mvtnorm, corpcor, plink2

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VEGAS2Pathway distribution

download

VEGAS2Pathway support

Maintainer

  • Aniket Mishra <>
  • Aniket Mishra <>

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Publications

Institution(s)

Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia

Funding source(s)

This work was supported by an ANZ Trustees PhD scholarship, the Australian National Health and Research Council and Australian Research Council fellowships.

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