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

Bioconductor version: Release (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>

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


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

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


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 2.8.0
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 (>= 3.5.0), 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
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Suggests knitr, BiocStyle, htmltools, clusterProfiler, macrophage,, magrittr, testthat (>= 2.1.0)
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Follow Installation instructions to use this package in your R session.

Source Package GeneTonic_2.8.0.tar.gz
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macOS Binary (x86_64) GeneTonic_2.8.0.tgz
macOS Binary (arm64) GeneTonic_2.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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