Glimma
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Glimma.
Interactive HTML graphics
Bioconductor version: 3.16
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("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")| 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 | 2.8.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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_2.8.0.tar.gz |
| Windows Binary | Glimma_2.8.0.zip |
| macOS Binary (x86_64) | Glimma_2.8.0.tgz |
| macOS Binary (arm64) | Glimma_2.8.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |