Welcome to GenRisk’s documentation!

GenRisk is a package that implements different gene-based scoring schemes to analyze and find significant genes within a phenotype in a population

Installation

Requirements

• plink >= 1.9

• R version >= 3.6.3

• python >= 3.

Package installation

Option 1: The latest release of GenRisk can be installed on python3+ with:

pip install genrisk

Option2: you can also install the package with the latest updates directly from GitHub with:

pip install git+https://github.com/AldisiRana/GenRisk.git

Citation

Rana Aldisi, Emadeldin Hassanin, Sugirthan Sivalingam, Andreas Buness, Hannah Klinkhammer, Andreas Mayr, Holger Fröhlich, Peter Krawitz, Carlo Maj, GenRisk: a tool for comprehensive genetic risk modeling, Bioinformatics, Volume 38, Issue 9, 1 May 2022, Pages 2651–2653, https://doi.org/10.1093/bioinformatics/btac152

Content

• Command Line Interface
  • genrisk score-genes
  • genrisk normalize
  • genrisk find-association
  • genrisk visualize
  • genrisk create-model
  • genrisk test-model
  • genrisk get-prs
• Pipeline functions
  • Gene scoring
  • Data normalization
  • Association analysis
  • Prediction model generation
• Utilities
  • draw_qqplot()
  • draw_manhattan()
• Model types
  • Regression models:
  • Classification models:
• Example use case
  • Annotated VCF
  • Gene-based scores
  • Association analysis
  • Machine learning models
• Real use case
  • LDL Phenotype
  • Alkaline phosphatase
  • Other phenotypes
• Methods Comparisons
• Computation information
  • Gene-based scoring and analysis
  • Prediction models generation

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Indices and tables

• Index

• Module Index

• Search Page