Package Recipe 'bioconductor-anota2seq'

recipe bioconductor-anota2seq

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/anota2seq.html
License:: GPL-3
Recipe:: /bioconductor-anota2seq/meta.yaml

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.

package bioconductor-anota2seq¶

Versions:

1.32.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0,

1.32.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.4.0-0

Depends:

on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-multtest >=2.66.0,<2.67.0
on bioconductor-qvalue >=2.42.0,<2.43.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-rcolorbrewer

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-anota2seq

to add into an existing workspace instead, run:

pixi add bioconductor-anota2seq

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-anota2seq

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-anota2seq

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-anota2seq:<tag>

(see bioconductor-anota2seq/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-anota2seq/README.html)