Glimma
This is the development version of Glimma; for the stable release version, see Glimma.
Interactive visualizations for gene expression analysis
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 2.23.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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, purrr, AnnotationHub, scRNAseq, scater, scran, scRNAseq |
| Linking To | |
| Enhances | |
| Depends On Me | RNAseq123 |
| Imports Me | affycoretools |
| Suggests Me | mastR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | Glimma_2.23.1.tgz |
| macOS Binary (sonoma-arm64) | Glimma_2.23.1.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 |