anota2seq
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see anota2seq.
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Bioconductor version: 3.10
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("anota2seq")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DifferentialExpression, GeneExpression, GeneRegulation, GenomeWideAssociation, ImmunoOncology, Microarray, Normalization, RNASeq, Regression, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.4.0), methods |
| Imports | multtest, qvalue, limma, DESeq2, edgeR, RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | anota2seq_1.8.0.tar.gz |
| Windows Binary | anota2seq_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | anota2seq_1.8.0.tgz |
| 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 |
| Old Source Packages for BioC 3.10 | Source Archive |