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iSEE extension for panels related to pathway analysis

Bioconductor version: Release (3.19)

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

Author: Kevin Rue-Albrecht [aut, cre] , Thomas Sandmann [ctb] , Charlotte Soneson [aut] , Federico Marini [ctb] , Denali Therapeutics [fnd]

Maintainer: Kevin Rue-Albrecht <kevinrue67 at>

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


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:

Integration with other panels HTML R Script
Introduction to iSEEpathways HTML R Script
Working with the Gene Ontology HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Infrastructure, Pathways, ShinyApps, Software, Visualization
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License Artistic-2.0
Depends iSEE
Imports ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment
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Suggests airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr,, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package iSEEpathways_1.2.0.tar.gz
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macOS Binary (x86_64) iSEEpathways_1.2.0.tgz
macOS Binary (arm64) iSEEpathways_1.2.0.tgz
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Source Repository (Developer Access) git clone
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