GTools

GTools implements QTL and eQTL analysis methods in R as an extension of the GeneticTools package to identify quantitative trait loci and associations between genetic variants and gene expression.

Key Features:

• R-package extension: Implemented in R as an extension of the GeneticTools package for genomic analyses.
• QTL and eQTL analysis: Supports quantitative trait loci (QTL) mapping and expression quantitative trait loci (eQTL) analysis.
• Linear Model Approach: Implements a linear-model-based testing framework aligned with standard practices in QTL/eQTL testing.
• Non-Parametrical Directional Testing Method: Implements the Non-Parametrical Directional Testing Method, a non-parametric approach that provides robustness to data outliers.
• Figure generation: Includes commands for generating publication-ready figures summarizing QTL and eQTL results.

Scientific Applications:

• QTL mapping: Identification of genetic loci associated with specific quantitative traits.
• eQTL analysis: Analysis of associations between genetic variants and gene expression levels.

Methodology:

Analysis methods explicitly include a linear-model testing framework and the Non-Parametrical Directional Testing Method, implemented in R as an extension of GeneticTools.