fission

This package is for version 3.11 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: 3.11

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 (from within R, enter citation("fission")):

Installation

To install this package, start R (version "4.0") 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 PDF

Details

biocViews ExperimentData, GEO, Genome, RNASeqData, Saccharomyces_cerevisiae_Data, SequencingData
Version 1.8.0
License LGPL
Depends R (>= 2.10), SummarizedExperiment
Imports
System Requirements
URL
See More
Suggests knitr
Linking To
Enhances
Depends On Me rnaseqGene, ROCpAI
Imports Me
Suggests Me
Links To Me
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Package Archives

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

Source Package fission_1.8.0.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/
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