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 (3.21)

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: ), Thomas Sandmann [ctb] (ORCID: ), Charlotte Soneson [aut] (ORCID: ), Federico Marini [ctb] (ORCID: ), 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")

# 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Infrastructure, Pathways, ShinyApps, Software, Visualization
Version	1.5.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
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

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.

Source Package	iSEEpathways_1.5.0.tar.gz
Windows Binary (x86_64)	iSEEpathways_1.5.0.zip
macOS Binary (x86_64)	iSEEpathways_1.5.0.tgz
macOS Binary (arm64)	iSEEpathways_1.5.0.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