PYRAMA: A tool for Meta-analysis of Genome Wide Association Studies



Analysis

Perform Robust or Standard GWAS analysis methods.

Meta-analysis

Combine multiple GWAS and perform Robust or Standard GWAS meta-analysis methods.

Bayesian

Perform Bayesian GWAS Meta-analysis.

Enrichment Analysis

Perform SNP-to-gene mapping and functional enrichment analysis.

Plots

Generate Manhattan, QQ, and Volcano plots for GWAS results.

©PYRAMA - Computational Genetics Group, Department of Computer Science and Biomedical Informatics, University of Thessaly

Discrete Phenotypes Analysis Results

Continuous Phenotypes Analysis Results

Single-study analysis using genotypes Analysis Results

Discrete Phenotypes Meta-Analysis Results

Continuous Phenotypes Meta-Analysis Results

Beta and SE Meta-Analysis Results

Bayesian Analysis/Meta-Analysis Results

g:SNPense results

g:GOSt Functional Enrichment Analysis Results

Manhattan Plot

QQ Plot

Volcano Plot

Help

Getting Started

Follow these steps to execute PYRAMA :

  1. Select your data input type: Discrete, Continuous, or BETA/SE.
  2. Upload your data file(s) in tab-separated format.
  3. Adjust analysis settings as needed.
  4. Click “Execute” to run the analysis and view results.

Input Formats

Make sure your files match one of these templates:

Example Data

Column Descriptions

Example Data

Column Descriptions

Example Data

Column Descriptions


Uploading Files



  1. Select your data type to reveal the relevant settings.

  2. Use the “Browse” file input button to select your file(s).

  3. Verify your file(s) structure matches one of the examples above.

Analysis Settings

Choose the right parameters for your study:

  • Inheritance Model: Additive, Dominant, Recessive models and Robust Methods
  • Effect Size Type: Odds Ratio, Cochran-Armitage Trend Test (CATT)
  • Heterogeneity Estimator: DerSimonian-Laird, Cochran-ANOVA (ANOVA) and Sidik-Jonkman (SJ)

Result Columns by Analysis Type

Continuous Phenotypes

BETA/SE Format

Discrete Phenotypes

Robust Methods

Bayesian Analysis/Meta-analysis

Plots

You can generate interactive Manhattan plots, VOlcano Plots and QQ-plots from your GWAS analysis/meta-analysis results.

Also, an interactive Manhattan plot from can be produced from the Enrichment Analysis results.

NOTE: If the input files are large, it takes some time to render interactive plots.

Welcome to PYRAMA!

PYRAMA: An open source tool for Robust Analysis and Meta-Analysis of Genome-Wide Association Studies

Correspondence: Dr. Pantelis G. Bagos (email: pbagos@compgen.org)

Download the source code of PYRAMA from GitHub

Computational Genetics Group

Main developer:

  • Georgios A. Manios - Department of Computer Science and Biomedical Informatics, University of Thessaly (email: gmanios@uth.gr)