fission

DOI: 10.18129/B9.bioc.fission    

This package is for version 3.14 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: 3.14

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>

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")

 

HTML	R Script	Fission yeast time course
PDF		Reference Manual

Details

biocViews	ExperimentData, GEO, Genome, RNASeqData, Saccharomyces_cerevisiae_Data, SequencingData
Version	1.14.0
License	LGPL
Depends	R (>= 2.10), SummarizedExperiment
Imports
LinkingTo
Suggests	knitr, markdown
SystemRequirements
Enhances
URL
Depends On Me	rnaseqGene, ROCpAI
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	fission_1.14.0.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