Glimma

This is the released version of Glimma; for the devel version, see Glimma.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Interactive visualizations for gene expression analysis

Bioconductor version: Release (3.23)

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>

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

Shian Su, Hasaru Kariyawasam, Oliver Voogd, Matthew Ritchie, Charity Law. Glimma: Interactive visualizations for gene expression analysis. doi:10.18129/B9.bioc.Glimma, R package version 2.22.1, https://bioconductor.org/packages/Glimma.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, Microarray, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version	2.22.1
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors
System Requirements
URL	https://github.com/hasaru-k/GlimmaV2
Bug Reports	https://github.com/hasaru-k/GlimmaV2/issues

Suggests	testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, purrr, AnnotationHub, scRNAseq, scater, scran, scRNAseq
Linking To
Enhances
Depends On Me	RNAseq123
Imports Me	affycoretools
Suggests Me	mastR
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Glimma_2.22.1.tar.gz
Windows Binary (x86_64)	Glimma_2.22.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	Glimma_2.22.1.tgz
macOS Binary (sonoma-arm64)	Glimma_2.22.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Glimma
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Glimma
Package Short Url	https://bioconductor.org/packages/Glimma/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive