Genomic signatures represent unique features within a species' DNA, enabling the differentiation of species and offering broad applications across various fields. This package provides essential tools for calculating these specific signatures, streamlining the process for researchers and offering a comprehensive and time-saving solution for genomic analysis.The amino acid contents are identified based on the work published by Sandberg et al. (2003) <doi:10.1016/s0378-1119(03)00581-x> and Xiao et al. (2015) <doi:10.1093/bioinformatics/btv042>. The Average Mutual Information Profiles (AMIP) values are calculated based on the work of Bauer et al. (2008) <doi:10.1186/1471-2105-9-48>. The Chaos Game Representation (CGR) plot visualization was done based on the work of Deschavanne et al. (1999) <doi:10.1093/oxfordjournals.molbev.a026048> and Jeffrey et al. (1990) <doi:10.1093/nar/18.8.2163>. The GC content is calculated based on the work published by Nakabachi et al. (2006) <doi:10.1126/science.1134196> and Barbu et al. (1956) <https://pubmed.ncbi.nlm.nih.gov/13363015>. The Oligonucleotide Frequency Derived Error Gradient (OFDEG) values are computed based on the work published by Saeed et al. (2009) <doi:10.1186/1471-2164-10-S3-S10>. The Relative Synonymous Codon Usage (RSCU) values are calculated based on the work published by Elek (2018) <https://urn.nsk.hr/urn:nbn:hr:217:686131>.
| Version: | 0.1.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | kaos, Biostrings, stats, entropy, seqinr |
| Published: | 2024-09-11 |
| DOI: | 10.32614/CRAN.package.GenomicSig |
| Author: | Mailarlinga [aut], Shashi Bhushan Lal [aut], Anu Sharma [aut, cre], Dwijesh Chandra Mishra [aut], Sudhir Srivastava [aut], Sanjeev Kumar [aut], Girish Kumar Jha [aut], Sayanti Guha Majumdar [aut], Megha Garg [aut], Sharanbasappa [ctb], Kabilan S [ctb] |
| Maintainer: | Anu Sharma <anu.sharma at icar.gov.in> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| CRAN checks: | GenomicSig results |
| Reference manual: | GenomicSig.pdf |
| Package source: | GenomicSig_0.1.0.tar.gz |
| Windows binaries: | r-devel: GenomicSig_0.1.0.zip, r-release: GenomicSig_0.1.0.zip, r-oldrel: GenomicSig_0.1.0.zip |
| macOS binaries: | r-release (arm64): GenomicSig_0.1.0.tgz, r-oldrel (arm64): GenomicSig_0.1.0.tgz, r-release (x86_64): GenomicSig_0.1.0.tgz, r-oldrel (x86_64): GenomicSig_0.1.0.tgz |
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