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fission

This is the development version of fission; for the stable 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: Development (3.18)

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 "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.21.0
License LGPL
Depends R (>= 2.10), SummarizedExperiment
Imports
Linking To
Suggests knitr, markdown
System Requirements
Enhances
URL
See More
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_1.21.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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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