{ "_id": "6a1d75bc1d7bb097a0a519fb", "Package": "SADEG", "Type": "Package", "Title": "Stability Analysis in Differentially Expressed Genes", "Version": "1.0.0", "Authors@R": "c(person(given = \"Babak\", family = \"Khorsand\", role = c(\"aut\", \"cre\"), email = \"khorsand@mail.um.ac.ir\"),\nperson(given = \"Ehsan\", family = \"Sadeghnezhad\", role = \"aut\"),\nperson(given = \"Javad\", family = \"Zahiri\", role = \"ths\"),\nperson(given = \"Mohsen\", family = \"Sharifi\", role = \"ths\"),\nperson(given = \"Hassan\", family = \"Zare-mayvan\", role = \"ths\"))", "Maintainer": "Babak Khorsand ", "Description": "We analyzed the nucleotide composition of genes with a\nspecial emphasis on stability of DNA sequences. Besides, in a\nvariety of different organisms unequal use of synonymous\ncodons, or codon usage bias, occurs which also show variation\namong genes in the same genome. Seemingly, codon usage bias is\naffected by both selective constraints and mutation bias which\nallows and enables us to examine and detect changes in these\ntwo evolutionary forces between genomes or along one genome.\nTherefore, we determined the codon adaptation index (CAI),\neffective number of codons (ENC) and codon usage analysis with\ncalculation of the relative synonymous codon usage (RSCU), and\nsubsequently predicted the translation efficiency and accuracy\nthrough GC-rich codon usages. Furthermore, we estimated the\nrelative stability of the DNA sequence following calculation of\nthe average free energy (Delta G) and Dimer base-stacking\nenergy level.", "License": "GPL", "RoxygenNote": "5.0.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-01 12:03:55 UTC", "User": "root" }, "Author": "Babak Khorsand [aut, cre], Ehsan Sadeghnezhad [aut], Javad\nZahiri [ths], Mohsen Sharifi [ths], Hassan Zare-mayvan [ths]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2017-01-12 23:43:16 UTC", "RemoteUrl": "https://github.com/cran/SADEG", "RemoteRef": "HEAD", "RemoteSha": "eadfbddae5a935a7c1d22f0b6703d73497ad4a31", "MD5sum": "456b520315ebec6ea3046d92fcd14b79", "_user": "cran", "_type": "src", "_file": "SADEG_1.0.0.tar.gz", "_fileid": "17dd96905484282da18f5530a317a11a316cde8a849caa3cdd8281124cb15724", "_filesize": 99164, "_sha256": "17dd96905484282da18f5530a317a11a316cde8a849caa3cdd8281124cb15724", "_created": "2026-06-01T12:03:55.000Z", "_published": 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