Package: sscu
Type: Package
Title: Strength of Selected Codon Usage
Version: 2.40.0
Date: 2016-12-1
Author: Yu Sun
Maintainer: Yu Sun <sunyu1357@gmail.com>
Description: 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.
Depends: R (>= 3.3)
Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>=
        0.16.1)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyLoad: yes
License: GPL (>= 2)
biocViews: Genetics, GeneExpression, WholeGenome
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:31:07 UTC
RemoteUrl: https://github.com/bioc/sscu
RemoteRef: RELEASE_3_22
RemoteSha: 76c92957bbf74f103759b02b248ab731cab5ad26
NeedsCompilation: no
Packaged: 2025-11-13 07:37:52 UTC; root
Built: R 4.5.2; ; 2025-11-13 07:39:23 UTC; windows
