Package: SADEG 1.0.0

Babak Khorsand

SADEG: Stability Analysis in Differentially Expressed Genes

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.

Authors:Babak Khorsand [aut, cre], Ehsan Sadeghnezhad [aut], Javad Zahiri [ths], Mohsen Sharifi [ths], Hassan Zare-mayvan [ths]

SADEG_1.0.0.tar.gz
SADEG_1.0.0.tar.gz(r-4.5-noble)SADEG_1.0.0.tar.gz(r-4.4-noble)
SADEG_1.0.0.tgz(r-4.4-emscripten)SADEG_1.0.0.tgz(r-4.3-emscripten)
SADEG.pdf |SADEG.html
SADEG/json (API)

# Install 'SADEG' in R:
install.packages('SADEG', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 14 scripts 92 downloads 1 mentions 14 exports 0 dependencies

Last updated 8 years agofrom:eadfbddae5. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-linuxOKDec 10 2024

Exports:SADEG.ACGTSADEG.CAISADEG.CodonUsageSADEG.DimerSADEG.DimerStackingEnergySADEG.EENCSADEG.GCSADEG.GC1SADEG.GC12SADEG.GC2SADEG.GC3SADEG.ReverseComplementSADEG.RSCUSADEG.StackingEnergy

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
SADEG.ACGTSADEG.ACGT
SADEG.CAISADEG.CAI
SADEG.CodonUsageSADEG.CodonUsage
SADEG.DimerSADEG.Dimer
SADEG.DimerStackingEnergySADEG.DimerStackingEnergy
SADEG.EENCSADEG.EENC
SADEG.GCSADEG.GC
SADEG.GC1SADEG.GC1
SADEG.GC12SADEG.GC12
SADEG.GC2SADEG.GC2
SADEG.GC3SADEG.GC3
SADEG.ReverseComplementSADEG.ReverseComplement
SADEG.RSCUSADEG.RSCU
SADEG.StackingEnergySADEG.StackingEnergy