sscu: Strength of Selected Codon Usage
Version 2.6.0

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.

AuthorYu Sun
Bioconductor views GeneExpression Genetics WholeGenome
Date of publicationNone
MaintainerYu Sun <sunyu1357@gmail.com>
LicenseGPL (>= 2)
Version2.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sscu")

Getting started

Package overview
sscu user manual (2.4.0)

Popular man pages

akashi_test: akashi test for codon usage
genomic_gc3: genomic gc3 for an multifasta genomic file
low_frequency_op: the function identify low frequency optimal codons
op_corre_CodonW: Identify optimal codons by using the correlative method from...
op_corre_NCprime: Identify optimal codons by using the correlative method from...
op_highly: Identify optimal codons by using the highly expressed genes...
op_highly_stats: statistics for the optimal codons
See all...

All man pages Function index File listing

Man pages

akashi_test: akashi test for codon usage
genomic_gc3: genomic gc3 for an multifasta genomic file
low_frequency_op: the function identify low frequency optimal codons
op_corre_CodonW: Identify optimal codons by using the correlative method from...
op_corre_NCprime: Identify optimal codons by using the correlative method from...
op_highly: Identify optimal codons by using the highly expressed genes...
op_highly_stats: statistics for the optimal codons
s_index: S index (Strength of Selected Codon Usage)
sscu-package: Strength of Selected Codon Usage

Functions

akashi_test Man page Source code
genomic_gc3 Man page Source code
low_frequency_op Man page Source code
op_corre_CodonW Man page Source code
op_corre_NCprime Man page Source code
op_highly Man page Source code
op_highly_stats Man page Source code
optimal_codon_statistics Man page
optimal_codons Man page
optimal_codons_table Man page
s_index Man page Source code
selected_codons Man page
sscu-package Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/akashi_test.R
R/genomic_gc3.R
R/low_frequency_op.R
R/op_corre_CodonW.R
R/op_corre_NCprime.R
R/op_highly.R
R/op_highly_stats.R
R/s_index.R
build
build/partial.rdb
inst
inst/akashi_test
inst/akashi_test/bifidos_alignments
inst/akashi_test/bifidos_alignments/0001.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0002.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0003.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0004.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0005.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0006.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0007.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0008.fas.ffn.mafft
inst/akashi_test/bifidos_alignments/0009.fas.ffn.mafft
inst/akashi_test/contingency_file_Gvag
inst/akashi_test/make_contingency_table.pl
inst/correlative_test
inst/correlative_test/Gvag.codonw
inst/correlative_test/LbDelBA1.NCprime
inst/sequences
inst/sequences/Gvag_genome_cds.ffn
inst/sequences/Gvag_highly.ffn
inst/sequences/L_kunkeei_genome_cds.ffn
inst/sequences/L_kunkeei_highly.ffn
inst/sequences/LbDelBA1_genome_cds.ffn
man
man/akashi_test.Rd
man/genomic_gc3.Rd
man/low_frequency_op.Rd
man/op_corre_CodonW.Rd
man/op_corre_NCprime.Rd
man/op_highly.Rd
man/op_highly_stats.Rd
man/s_index.Rd
man/sscu-package.Rd
vignettes
vignettes/sscu.Rmd
sscu documentation built on May 20, 2017, 9:45 p.m.

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