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GPflexViz - Graphical Visualizations Related to Genomic Prediction

Provides flexible tools for the visualization of genomic data. Supports interactive and static plots tailored for presentations and publications, with customizable features like colors, themes, and annotations to align with specific analytical and presentation goals.

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3.88 score 3 stars 1 scripts 474 downloads

iPRSue - Individual Polygenic Risk Score Uncertainty Estimation

Provides tools for estimating uncertainty in individual polygenic risk scores (PRSs) using both sampling-based and analytical methods, as well as the Best Linear Unbiased Estimator (BLUE). These methods quantify variability in PRS estimates for both binary and quantitative traits. See Henderson (1975) <doi:10.2307/2529430> for more details.

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3.65 score 1 scripts 435 downloads

GxEprs - Genotype-by-Environment Interaction in Polygenic Score Models

A novel PRS model is introduced to enhance the prediction accuracy by utilising GxE effects. This package performs Genome Wide Association Studies (GWAS) and Genome Wide Environment Interaction Studies (GWEIS) using a discovery dataset. The package has the ability to obtain polygenic risk scores (PRSs) for a target sample. Finally it predicts the risk values of each individual in the target sample. Users have the choice of using existing models (Li et al., 2015) <doi:10.1093/annonc/mdu565>, (Pandis et al., 2013) <doi:10.1093/ejo/cjt054>, (Peyrot et al., 2018) <doi:10.1016/j.biopsych.2017.09.009> and (Song et al., 2022) <doi:10.1038/s41467-022-32407-9>, as well as newly proposed models for genomic risk prediction (refer to the URL for more details).

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3.30 score 2 stars 2 scripts 569 downloads