To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("anota2seq")

In most cases, you don't need to download the package archive at all.

anota2seq

DOI: 10.18129/B9.bioc.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 (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("anota2seq")

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, Microarray, Normalization, RNASeq, Regression, Sequencing, Software
Version 1.1.0
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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package anota2seq_1.1.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) anota2seq_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/anota2seq
Package Short Url http://bioconductor.org/packages/anota2seq/
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