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iSEEpathways

iSEE extension for panels related to pathway analysis


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") 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")
Integration with other panels HTML R Script
Introduction to iSEEpathways HTML R Script
Working with the Gene Ontology HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Infrastructure, Pathways, ShinyApps, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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
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Build Report Build Report

Package Archives

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

Source Package iSEEpathways_1.0.0.tar.gz
Windows Binary iSEEpathways_1.0.0.zip
macOS Binary (x86_64) iSEEpathways_1.0.0.tgz
macOS Binary (arm64) iSEEpathways_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/iSEEpathways
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/iSEEpathways
Bioc Package Browser https://code.bioconductor.org/browse/iSEEpathways/
Package Short Url https://bioconductor.org/packages/iSEEpathways/
Package Downloads Report Download Stats