fission
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see fission.
RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014.
Bioconductor version: 3.13
This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("fission")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fission")
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("fission")| Fission yeast time course | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, GEO, Genome, RNASeqData, Saccharomyces_cerevisiae_Data, SequencingData |
| Version | 1.12.0 |
| License | LGPL |
| Depends | R (>= 2.10), SummarizedExperiment |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | rnaseqGene, ROCpAI |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fission_1.12.0.tar.gz |
| Windows Binary | |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/fission |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fission |
| Package Short Url | https://bioconductor.org/packages/fission/ |
| Package Downloads Report | Download Stats |