HybridExpress

An R package for comparative transcriptomic analyses of hybrids and their progenitors

Summary

The goal of HybridExpress is to perform comparative transcriptomic analyses of hybrids relative to their progenitor species (a.k.a. experimental trios). The package features:

1. Calculation of midparent expression values, which are in silico samples obtained from the mean, sum, or weighted mean of random sample pairs from each parent;

2. Exploratory analyses of sample grouping with PCA plots and heatmaps of hierarchically-clustered pairwise sample correlations;

3. Identification of differentially expressed genes between hybrids and their progenitor species, hybrids and midparent values, and the two parents. If spike-in standards are available, HybridExpress uses them to normalize the count data by transcriptome size;

4. Classification of genes in expression-based categories and classes based on Rapp et al. (2009). The 12 expression categories proposed by Rapp et al. (2009) are grouped into 5 major classes (transgressive up-regulation, transgressive down-regulation, additivity, expression-level dominance toward parent 1, and expression-level dominance toward parent 2);

5. Functional analyses through the identification of overrepresented functional terms for gene sets of interest.