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iSEEpathways

iSEE extension for panels related to pathway analysis

Bioconductor version: 3.23 · Package version: 1.10.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("iSEEpathways")

Details

MaintainerKevin Rue-Albrecht <kevinrue67@gmail.com>
AuthorKevin Rue-Albrecht [aut, cre] (ORCID: <https://orcid.org/0000-0003-3899-3872>), Thomas Sandmann [ctb] (ORCID: <https://orcid.org/0000-0002-6601-8890>), Charlotte Soneson [aut] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Federico Marini [ctb] (ORCID: <https://orcid.org/0000-0003-3252-7758>), Denali Therapeutics [fnd]
LicenseArtistic-2.0
URLhttps://github.com/iSEE/iSEEpathways
Bug Reportshttps://support.bioconductor.org/t/iSEEpathways
Downloads rank381
Source branchRELEASE_3_23
biocViewsDifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Infrastructure, Pathways, ShinyApps, Software, Visualization

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageiSEEpathways_1.10.0.tar.gz
Windows binary (x86_64)iSEEpathways_1.10.0.zip
macOS binary (arm64)iSEEpathways_1.10.0.tgz
macOS binary (x86_64)iSEEpathways_1.10.0.tgz
Dependencies

Depends: iSEE

Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment

Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0)