Glimma

DOI: 10.18129/B9.bioc.Glimma    

Interactive HTML graphics

Bioconductor version: Release (3.15)

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 "4.2") 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 2.6.0
In Bioconductor since BioC 3.3 (R-3.3) (6.5 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_2.6.0.tar.gz
Windows Binary Glimma_2.6.0.zip
macOS Binary (x86_64) Glimma_2.6.0.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

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