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SADEG
View on CRAN: Click
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Download and install SADEG package within the R console
Install from CRAN:
install.packages("SADEG")
Install from Github:
library("remotes")
install_github("cran/SADEG")
Install by package version:
library("remotes")
install_version("SADEG", "1.0.0")
Attach the package and use:
library("SADEG")
Maintained by
Babak Khorsand
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-01-13
Latest Update: 2017-01-13
Description:
We analyzed the nucleotide composition of genes with a special emphasis on stability of DNA sequences. Besides, in a variety of different organisms unequal use of synonymous codons, or codon usage bias, occurs which also show variation among genes in the same genome. Seemingly, codon usage bias is affected by both selective constraints and mutation bias which allows and enables us to examine and detect changes in these two evolutionary forces between genomes or along one genome. Therefore, we determined the codon adaptation index (CAI), effective number of codons (ENC) and codon usage analysis with calculation of the relative synonymous codon usage (RSCU), and subsequently predicted the translation efficiency and accuracy through GC-rich codon usages. Furthermore, we estimated the relative stability of the DNA sequence following calculation of the average free energy (Delta G) and Dimer base-stacking energy level.
How to cite:
Babak Khorsand (2017). SADEG: Stability Analysis in Differentially Expressed Genes. R package version 1.0.0, https://cran.r-project.org/web/packages/SADEG
Previous versions and publish date:
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Other R packages that SADEG depends,
imports, suggests or enhances
Functions, R codes and Examples using
the SADEG R package
Some associated functions: SADEG.ACGT . SADEG.CAI . SADEG.CodonUsage . SADEG.Dimer . SADEG.DimerStackingEnergy . SADEG.EENC . SADEG.GC . SADEG.GC1 . SADEG.GC12 . SADEG.GC2 . SADEG.GC3 . SADEG.RSCU . SADEG.ReverseComplement . SADEG.StackingEnergy .
Some associated R codes: ATCG.R . CAI.R . CodonUsage.R . Dimer.R . DimerStackingEnergy.R . ENC.R . GC.R . GC1.R . GC12.R . GC2.R . GC3.R . RSCU.R . ReverseComplement.R . StackingEnergy.R . Full SADEG package functions and examples
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