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]
, 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 "4.5") 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")| Integration with other panels | HTML | R Script |
| Introduction to iSEEpathways | HTML | R Script |
| Working with the Gene Ontology | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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.
| Source Package | iSEEpathways_1.6.0.tar.gz |
| Windows Binary (x86_64) | iSEEpathways_1.6.0.zip |
| macOS Binary (x86_64) | iSEEpathways_1.6.0.tgz |
| macOS Binary (arm64) | iSEEpathways_1.6.0.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 |