Package: anota2seq
Version: 1.32.0
Title: Generally applicable transcriptome-wide analysis of
        translational efficiency using anota2seq
Author: Christian Oertlin <christian.oertlin@ki.se>, Julie Lorent
        <julie.lorent@ki.se>, Ola Larsson <ola.larsson@ki.se>
Maintainer: Christian Oertlin <christian.oertlin@ki.se>, Ola Larsson
 <ola.larsson@ki.se>
Description: 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.
Depends: R (>= 3.4.0), methods
License: GPL-3
LazyData: yes
LazyLoad: yes
Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
        graphics, stats, utils, SummarizedExperiment
biocViews: ImmunoOncology, GeneExpression, DifferentialExpression,
        Microarray,GenomeWideAssociation, BatchEffect, Normalization,
        RNASeq, Sequencing, GeneRegulation, Regression
NeedsCompilation: no
Packaged: 2025-11-11 16:39:36 UTC; root
Suggests: BiocStyle,knitr
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:41:23 UTC
RemoteUrl: https://github.com/bioc/anota2seq
RemoteRef: RELEASE_3_22
RemoteSha: 8720150a119edcc8ab237009b593ba3253e20c1c
Built: R 4.5.2; ; 2025-11-11 16:44:58 UTC; windows
