iSEEde

DOI: 10.18129/B9.bioc.iSEEde  

iSEE extension for panels related to differential expression 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 differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression 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] , Denali Therapeutics [fnd]

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("iSEEde")

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("iSEEde")

 

HTML	R Script	Introduction to iSEEde
HTML	R Script	Rounding numeric values
HTML	R Script	Supported differential expression methods
HTML	R Script	Using annotations to facilitate interactive exploration
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, Infrastructure, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	iSEE
Imports	DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment
LinkingTo
Suggests	airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/iSEE/iSEEde
BugReports	https://support.bioconductor.org/t/iSEEde
Depends On Me
Imports Me
Suggests Me	iSEEpathways
Links To Me
Build Report

Package Archives

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

Source Package	iSEEde_1.0.0.tar.gz
Windows Binary	iSEEde_1.0.0.zip
macOS Binary (x86_64)	iSEEde_1.0.0.tgz
macOS Binary (arm64)	iSEEde_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/iSEEde
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/iSEEde
Bioc Package Browser	https://code.bioconductor.org/browse/iSEEde/
Package Short Url	https://bioconductor.org/packages/iSEEde/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive