Bioconductor/R package trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession. This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.
Keywords for this software
References in zbMATH (referenced in 1 article )
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- Bucur, Ioan Gabriel; Claassen, Tom; Heskes, Tom: Large-scale local causal inference of gene regulatory relationships (2019)