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Glimma

This is the development version of Glimma; for the stable release version, see Glimma.

Interactive HTML graphics

Bioconductor version: Development (3.18)

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>

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, GeneExpression, Microarray, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version 2.11.0
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
Linking To
Suggests testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran
System Requirements
Enhances
URL https://github.com/hasaru-k/GlimmaV2
Bug Reports https://github.com/hasaru-k/GlimmaV2/issues
See More
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_2.11.0.tar.gz
Windows Binary Glimma_2.11.0.zip (64-bit only)
macOS Binary (x86_64) Glimma_2.11.0.tgz
macOS Binary (arm64)
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