Package: Glimma 2.23.1

Shian Su

Glimma: Interactive visualizations for gene expression analysis

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.

Authors:Shian Su [aut, cre], Hasaru Kariyawasam [aut], Oliver Voogd [aut], Matthew Ritchie [aut], Charity Law [aut], Stuart Lee [ctb], Isaac Virshup [ctb]

Glimma_2.23.1.tar.gz
Glimma_2.23.1.zip(r-4.7)Glimma_2.23.1.zip(r-4.6)Glimma_2.23.1.zip(r-4.5)
Glimma_2.23.1.tgz(r-4.6-any)Glimma_2.23.1.tgz(r-4.5-any)
Glimma_2.23.1.tar.gz(r-4.7-any)Glimma_2.23.1.tar.gz(r-4.6-any)
Glimma_2.23.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Glimma/json (API)
NEWS

# Install 'Glimma' in R:
install.packages('Glimma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hasaru-k/glimmav2/issues

On BioConductor:Glimma-2.23.1(bioc 3.24)Glimma-2.21.0(bioc 3.23)

differentialexpressiongeneexpressionmicroarrayreportwritingrnaseqsequencingvisualizationdifferential-expressioninteractive-visualizations

10.81 score 35 stars 2 packages 748 scripts 1.8k downloads 17 mentions 9 exports 71 dependencies

Last updated from:59966a16c6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR234
linux-devel-x86_64NOTE496
source / vignettesOK630
linux-release-x86_64NOTE511
macos-release-arm64NOTE292
macos-oldrel-arm64NOTE349
windows-develNOTE1519
windows-releaseNOTE1410
windows-oldrelNOTE1492
wasm-releaseOK209

Exports:glimmaMAglimmaMDglimmaMDSglimmaVolcanoglimmaXYglMDPlotglMDRmdglMDSPlotglXYPlot

Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemclicodetoolscpp11DelayedArrayDESeq2digestedgeRevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetsIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemimeR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodSummarizedExperimenttinytexvctrsviridisLitewithrxfunXVectoryaml

DESeq2

Rendered fromDESeq2.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-09-23
Started: 2020-10-21

Introduction using limma or edgeR

Rendered fromlimma_edger.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-03-08
Started: 2020-10-21

Single Cells with edgeR

Rendered fromsingle_cell_edger.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-03-08
Started: 2021-09-20

Readme and manuals

Help Manual

Help pageTopics
Numeric to hex colour converteras.hexcol
Glimma: interactive graphics from limmaGlimma-package Glimma glimma
Glimma MA PlotglimmaMA glimmaMD
Glimma MA PlotglimmaMA.DESeqDataSet
Glimma MA PlotglimmaMA.DGEExact
Glimma MA PlotglimmaMA.DGELRT
Glimma MA PlotglimmaMA.MArrayLM
Glimma MDS PlotglimmaMDS
Glimma MDS PlotglimmaMDS.default
Glimma MDS PlotglimmaMDS.DESeqDataSet
Glimma MDS PlotglimmaMDS.DGEList
Glimma Volcano PlotglimmaVolcano
Glimma Volcano PlotglimmaVolcano.DESeqDataSet
Glimma Volcano PlotglimmaVolcano.DGEExact
Glimma Volcano PlotglimmaVolcano.DGELRT
Glimma Volcano PlotglimmaVolcano.MArrayLM
Glimma XY PlotglimmaXY
Glimma MD PlotglMDPlot
Glimma MD PlotglMDPlot.default
Glimma MD PlotglMDPlot.DESeqDataSet
Glimma MD PlotglMDPlot.DESeqResults
Glimma MD PlotglMDPlot.DGEExact
Glimma MD PlotglMDPlot.DGELRT
Glimma MD PlotglMDPlot.MArrayLM
glMDPlot Rmarkdown link and instructionsglMDRmd
Glimma MDS PlotglMDSPlot
Glimma MDS PlotglMDSPlot.default
Glimma MDS PlotglMDSPlot.DESeqDataSet
Glimma MDS PlotglMDSPlot.DGEList
Glimma XY PlotglXYPlot
Hexcode coloursis.hex