iSEEpathways

DOI: 10.18129/B9.bioc.iSEEpathways  

This is the development version of iSEEpathways; for the stable release version, see iSEEpathways.

iSEE extension for panels related to pathway analysis

Bioconductor version: Development (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 gmail.com>

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

biocViews	DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Infrastructure, Pathways, ShinyApps, Software, Visualization
Version	1.1.0
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
LinkingTo
Suggests	airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/iSEE/iSEEpathways
BugReports	https://support.bioconductor.org/t/iSEEpathways
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	iSEEpathways_1.1.0.tar.gz
Windows Binary	iSEEpathways_1.1.0.zip
macOS Binary (x86_64)	iSEEpathways_1.1.0.tgz
macOS Binary (arm64)
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