Glimma

DOI: 10.18129/B9.bioc.Glimma  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see Glimma.

Interactive HTML graphics

Bioconductor version: 3.17

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

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	2.10.0
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_2.10.0.tar.gz
Windows Binary	Glimma_2.10.0.zip
macOS Binary (x86_64)	Glimma_2.10.0.tgz
macOS Binary (arm64)	Glimma_2.10.0.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