Glimma
Interactive visualizations for gene expression analysis
Bioconductor version: Release (3.19)
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("Glimma")):
Installation
To install this package, start R (version "4.4") 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")| DESeq2 | HTML | R Script |
| Introduction using limma or edgeR | HTML | R Script |
| Single Cells with edgeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Microarray, RNASeq, ReportWriting, Sequencing, Software, Visualization |
| Version | 2.14.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0) |
| Imports | htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors |
| System Requirements | |
| URL | https://github.com/hasaru-k/GlimmaV2 |
| Bug Reports | https://github.com/hasaru-k/GlimmaV2/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran |
| Linking To | |
| Enhances | |
| Depends On Me | RNAseq123 |
| Imports Me | affycoretools |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Glimma_2.14.0.tar.gz |
| Windows Binary (x86_64) | Glimma_2.14.0.zip |
| macOS Binary (x86_64) | Glimma_2.14.0.tgz |
| macOS Binary (arm64) | Glimma_2.14.0.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 |