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

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Bioconductor version: Development (3.19)

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

Author: Federico Marini [aut, cre] , Annekathrin Ludt [aut]

Maintainer: Federico Marini <marinif at uni-mainz.de>

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


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:

The GeneTonic User's Guide HTML R Script
Reference Manual PDF


biocViews Annotation, DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ReportWriting, ShinyApps, Software, Transcription, Transcriptomics, Visualization
Version 2.7.2
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2, ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork
System Requirements
URL https://github.com/federicomarini/GeneTonic
Bug Reports https://github.com/federicomarini/GeneTonic/issues
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Suggests knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GeneTonic_2.7.2.tar.gz
Windows Binary GeneTonic_2.7.2.zip (64-bit only)
macOS Binary (x86_64) GeneTonic_2.7.1.tgz
macOS Binary (arm64) GeneTonic_2.7.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneTonic
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneTonic
Bioc Package Browser https://code.bioconductor.org/browse/GeneTonic/
Package Short Url https://bioconductor.org/packages/GeneTonic/
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