Comparative analysis of RNA-seq data for hybrids and their progenitors

Documentation for package ‘HybridExpress’ version 1.0.1

add_midparent_expression	Add midparent expression to 'SummarizedExperiment' object
add_size_factors	Add size factors to normalize count data by library size or by biomass
deg_counts	Data frame with frequencies (absolute and relative) of DEGs per contrast
deg_list	List of differentially expressed genes for all contrasts
expression_partitioning	Partition genes in groups based on their expression patterns
get_deg_counts	Get a count table of differentially expressed genes per contrast
get_deg_list	Get a table of differential expression expression statistics with DESeq2
go_chlamy	Data frame with GO terms annotated to each gene of Chlamydomonas reinhardtii
ora	Perform overrepresentation analysis for a set of genes
pca_plot	Perform a principal component analysis (PCA) and plot PCs
plot_expression_partitions	Plot expression partitions
plot_expression_triangle	Plot a triangle of comparisons of DEG sets among generations
plot_partition_frequencies	Plot a barplot of gene frequencies per expression partition
plot_samplecor	Plot a heatmap of pairwise sample correlations with hierarchical clustering
se_chlamy	Expression data (in counts) for 3 Chlamydomonas lines (P1, P2, and F1)