anota2seq
This is the development version of anota2seq; for the stable release version, see anota2seq.
All Bioconductor versions of anota2seq
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Bioconductor version: 3.24 · Package version: 1.35.0
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>, Ola Larsson <ola.larsson at ki.se>
Citation
From within R, enter citation("anota2seq"):
Christian Oertlin, Julie Lorent, Ola Larsson. anota2seq: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq. doi:10.18129/B9.bioc.anota2seq, R package version 1.35.0, https://bioconductor.org/packages/anota2seq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("anota2seq")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.35.0 |
| License | GPL-3 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 980 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, DifferentialExpression, GeneExpression, GeneRegulation, GenomeWideAssociation, ImmunoOncology, Microarray, Normalization, RNASeq, Regression, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/anota2seq/ |
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | anota2seq_1.35.0.tar.gz |
| Windows binary (x86_64) | anota2seq_1.35.0.zip |
| macOS binary (arm64) | anota2seq_1.35.0.tgz |
| macOS binary (x86_64) | anota2seq_1.35.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/anota2seq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/anota2seq |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.4.0), methods
Imports: multtest, qvalue, limma, DESeq2, edgeR, RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment
Reverse dependencies
Imports Me (1): postNet