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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: