anota2seq

DOI: 10.18129/B9.bioc.anota2seq    

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Bioconductor version: Release (3.13)

anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks.

Author: Christian Oertlin <christian.oertlin at ki.se>, Julie Lorent <julie.lorent at ki.se>, Ola Larsson <ola.larsson at ki.se>

Maintainer: Christian Oertlin <christian.oertlin at ki.se>, Julie Lorent <julie.lorent at ki.se>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("anota2seq")

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("anota2seq")

 

PDF	R Script	Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, DifferentialExpression, GeneExpression, GeneRegulation, GenomeWideAssociation, ImmunoOncology, Microarray, Normalization, RNASeq, Regression, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	GPL-3
Depends	R (>= 3.4.0), methods
Imports	multtest, qvalue, limma, DESeq2, edgeR, RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment
LinkingTo
Suggests	BiocStyle, knitr
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Package Archives

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

Source Package	anota2seq_1.14.0.tar.gz
Windows Binary	anota2seq_1.14.0.zip
macOS 10.13 (High Sierra)	anota2seq_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/anota2seq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/anota2seq
Package Short Url	https://bioconductor.org/packages/anota2seq/
Package Downloads Report	Download Stats