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This is the development version of ideal; for the stable release version, see ideal.

Interactive Differential Expression AnaLysis

Bioconductor version: Development (3.20)

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.

Author: Federico Marini [aut, cre]

Maintainer: Federico Marini <marinif at>

Citation (from within R, enter citation("ideal")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ideal User's Guide HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, ShinyApps, Software, Visualization
Version 1.29.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License MIT + file LICENSE
Depends topGO
Imports DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods
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Suggests testthat, BiocStyle, markdown, airway,, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
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Follow Installation instructions to use this package in your R session.

Source Package ideal_1.29.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ideal_1.29.0.tgz
macOS Binary (arm64) ideal_1.29.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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