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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>

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

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")
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 HTML R Script
Reference Manual PDF
NEWS Text

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
System Requirements
URL https://github.com/iSEE/iSEEde
Bug Reports https://support.bioconductor.org/t/iSEEde
See More
Suggests airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me iSEEpathways
Links To Me
Build Report 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 (64-bit only)
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