RNAseq123
This is the released version of RNAseq123; for the devel version, see RNAseq123.
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Bioconductor version: Release (3.23)
R package that supports the F1000Research workflow article on RNA-seq analysis using limma, Glimma and edgeR by Law et al. (2016).
Author: Charity Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon Smyth and Matthew Ritchie
Maintainer: Matthew Ritchie <mritchie at wehi.edu.au>
citation("RNAseq123")):
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")
BiocManager::install("RNAseq123")
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("RNAseq123")| A guide to creating design matrices for gene expression experiments (English version) | HTML | R Script |
| RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR (Chinese version) | HTML | R Script |
| RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR (English version) | HTML | R Script |
Details
| biocViews | GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.36.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.0), Glimma(>= 1.1.9), limma, edgeR, gplots, RColorBrewer, Mus.musculus, R.utils, TeachingDemos, statmod, BiocWorkflowTools |
| Imports | |
| System Requirements | |
| URL | https://f1000research.com/articles/5-1408/v3 |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RNAseq123_1.36.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/RNAseq123 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RNAseq123 |
| Package Short Url | https://bioconductor.org/packages/RNAseq123/ |
| Package Downloads Report | Download Stats |