Glimma
Interactive visualizations for gene expression analysis
Bioconductor version: 3.24 · Package version: 2.23.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Glimma")Details
| Maintainer | Shian Su <su.s@wehi.edu.au> |
| Author | Shian Su [aut, cre], Hasaru Kariyawasam [aut], Oliver Voogd [aut], Matthew Ritchie [aut], Charity Law [aut], Stuart Lee [ctb], Isaac Virshup [ctb] |
| License | GPL-3 |
| URL | https://github.com/hasaru-k/GlimmaV2 |
| Bug Reports | https://github.com/hasaru-k/GlimmaV2/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, Microarray, RNASeq, ReportWriting, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/Glimma/ |
Citation
From within R, enter citation("Glimma"):
Shian Su, Hasaru Kariyawasam, Oliver Voogd, Matthew Ritchie, Charity Law. Glimma: Interactive visualizations for gene expression analysis. doi:10.18129/B9.bioc.Glimma, R package version 2.23.1, https://bioconductor.org/packages/Glimma.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Glimma_2.23.1.tar.gz |
| Windows binary (x86_64) | Glimma_2.23.1.zip |
| macOS binary (arm64) | Glimma_2.23.1.tgz |
| macOS binary (x86_64) | Glimma_2.23.1.tgz |
Dependencies
Depends: R (>= 4.0.0)
Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors
Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, purrr, AnnotationHub, scRNAseq, scater, scran, scRNAseq
Reverse dependencies
Depends On Me (1): RNAseq123
Imports Me (1): affycoretools
Suggests Me (1): mastR