Package index • HybridExpress

All functions

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)