The ideal package

Main functions and info on the ideal package

ideal()

ideal: Interactive Differential Expression Analysis

ideal-pkg

ideal: Interactive Differential Expression Analysis

Working with Differentially Expressed genes

Functions for extracting and plotting overviews of Differentially Expressed genes

deseqresult2DEgenes()

Generate a tidy table with the DE genes from the results of DESeq

deseqresult2tbl()

Generate a tidy table with the results of DESeq

plot_ma()

MA-plot from base means and log fold changes

plot_volcano()

Volcano plot for log fold changes and log p-values

ggplotCounts()

Plot normalized counts for a gene

Functional interpretation

Functions for working performing functional interpretation

goseqTable()

Extract functional terms enriched in the DE genes, based on goseq

read_gmt()

Read in a GMT file

sig_heatmap()

Plot a heatmap of the gene signature on the data

Miscellaneous functions

Miscellaneous functions used in the ideal package

sepguesser()

Make an educated guess on the separator character

wrapup_for_iSEE()

wrapup_for_iSEE