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Bioconductor - iSEEpathways

iSEEpathways

This is the released version of iSEEpathways; for the devel version, see iSEEpathways.

iSEE extension for panels related to pathway analysis

Bioconductor version: Release (3.21)

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] ORCID: 0000-0003-3899-3872 , Thomas Sandmann [ctb] ORCID: 0000-0002-6601-8890 , Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169 , Federico Marini [ctb] ORCID: 0000-0003-3252-7758 , Denali Therapeutics [fnd]

Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>

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

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("iSEEpathways")

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

Documentation

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

browseVignettes("iSEEpathways")
Details biocViews DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Infrastructure, Pathways, ShinyApps, Software, Visualization Version 1.6.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) License Artistic-2.0 Depends iSEE Imports ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment System Requirements URL https://github.com/iSEE/iSEEpathways Bug Reports https://support.bioconductor.org/t/iSEEpathways See More Suggests airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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