# Interactive Differential Expression AnaLysis

## Documentation for package ‘ideal’ version 2.5.0

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

## Help Pages

ideal-package | ideal: Interactive Differential Expression Analysis
deprecated | Deprecated functions in ideal
deseqresult2DEgenes | Generate a tidy table with the DE genes from the results of DESeq
deseqresult2tbl | Generate a tidy table with the results of DESeq
ggplotCounts | Plot normalized counts for a gene
goseqTable | Extract functional terms enriched in the DE genes, based on goseq
ideal | ideal: Interactive Differential Expression Analysis
ideal-pkg | ideal: Interactive Differential Expression Analysis
plot_ma | MA-plot from base means and log fold changes
plot_volcano | Volcano plot for log fold changes and log p-values
read_gmt | Read in a GMT file
sepguesser | Make an educated guess on the separator character
sig_heatmap | Plot a heatmap of the gene signature on the data
wrapup_for_iSEE | wrapup_for_iSEE