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anota2seq

This is the development version of anota2seq; for the stable release version, see anota2seq.

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("anota2seq")):

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

Details

biocViews BatchEffect, DifferentialExpression, GeneExpression, GeneRegulation, GenomeWideAssociation, ImmunoOncology, Microarray, Normalization, RNASeq, Regression, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-3
Depends R (>= 3.4.0), methods
Imports multtest, qvalue, limma, DESeq2, edgeR, RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment
Linking To
Suggests BiocStyle, knitr
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Package Archives

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

Source Package anota2seq_1.23.0.tar.gz
Windows Binary anota2seq_1.23.0.zip
macOS Binary (x86_64) anota2seq_1.23.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/anota2seq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/anota2seq
Bioc Package Browser https://code.bioconductor.org/browse/anota2seq/
Package Short Url https://bioconductor.org/packages/anota2seq/
Package Downloads Report Download Stats