recipe bioconductor-sscu

Strength of Selected Codon Usage

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/sscu.html

License:

GPL (>= 2)

Recipe:

/bioconductor-sscu/meta.yaml

Links:

biotools: sscu, doi: 10.1038/nmeth.3252

The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp's method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) The package can detect the strength of translational accuracy selection by Akashi's test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi's test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function low_frequency_op in the package. The function try to find the low frequency optimal codons, among all the optimal codons identified by the op_highly function.

package bioconductor-sscu

(downloads) docker_bioconductor-sscu

versions:
2.32.0-0,  2.30.0-0,  2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0, 

2.32.0-0,  2.30.0-0,  2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.12.0-0,  2.10.0-0,  2.8.0-0,  2.6.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends r-base:

>=4.3,<4.4.0a0

depends r-seqinr:

>=3.1-3

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-sscu

and update with::

   mamba update bioconductor-sscu

To create a new environment, run:

mamba create --name myenvname bioconductor-sscu

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-sscu/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda 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-sscu/README.html)