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

## Documentation for package ‘HybridExpress’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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)