Glimma

DOI: 10.18129/B9.bioc.Glimma  

Interactive visualizations for gene expression analysis

Bioconductor version: Release (3.18)

This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.

Author: Shian Su [aut, cre], Hasaru Kariyawasam [aut], Oliver Voogd [aut], Matthew Ritchie [aut], Charity Law [aut], Stuart Lee [ctb], Isaac Virshup [ctb]

Maintainer: Shian Su <su.s at wehi.edu.au>

Installation

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

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

BiocManager::install("Glimma")

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("Glimma")

 

HTML	R Script	DESeq2
HTML	R Script	Introduction using limma or edgeR
HTML	R Script	Single Cells with edgeR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, Microarray, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version	2.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran
SystemRequirements
Enhances
URL	https://github.com/hasaru-k/GlimmaV2
BugReports	https://github.com/hasaru-k/GlimmaV2/issues
Depends On Me	RNAseq123
Imports Me	affycoretools
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Glimma_2.12.0.tar.gz
Windows Binary	Glimma_2.12.0.zip
macOS Binary (x86_64)	Glimma_2.12.0.tgz
macOS Binary (arm64)	Glimma_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Glimma
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Glimma
Bioc Package Browser	https://code.bioconductor.org/browse/Glimma/
Package Short Url	https://bioconductor.org/packages/Glimma/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive