Package: GenomicSig 0.1.0
Anu Sharma
GenomicSig: Computation of Genomic Signatures
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>.
Authors:
GenomicSig_0.1.0.tar.gz
GenomicSig_0.1.0.tar.gz(r-4.5-noble)GenomicSig_0.1.0.tar.gz(r-4.4-noble)
GenomicSig_0.1.0.tgz(r-4.4-emscripten)GenomicSig_0.1.0.tgz(r-4.3-emscripten)
GenomicSig.pdf |GenomicSig.html✨
GenomicSig/json (API)
# Install 'GenomicSig' in R: |
install.packages('GenomicSig', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- Genomicdata - Nucleotide sequence Data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:52bece5bce. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 11 2024 |
R-4.5-linux | OK | Nov 11 2024 |
Exports:AminoAcidContentAMIPCGRGC_contentOFDEGRSCU
Dependencies:ade4askpassBiocGenericsBiostringsclicolorspacecrayoncurlentropyfansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonlitekaoslabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangS4VectorsscalessegmentedseqinrspstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Amino Acid Content | AminoAcidContent |
Average Mutual Information Profile (AMIP) | AMIP |
Chaos Game Representation | CGR |
GC content of nucleic acid sequences | GC_content |
Nucleotide sequence Data | Genomicdata |
Oligonucleotide Frequency Derived Error Gradient | OFDEG |
Relative Synonymous Codon Usage | RSCU |