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: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]

GenomicSig_0.1.0.tar.gz
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GenomicSig.pdf |GenomicSig.html✨
GenomicSig/json (API)

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6 exports 0.00 score 58 dependencies 6 scripts 6 downloads

Last updated 6 days agofrom:52bece5bce. Checks:OK: 2. Indexed: yes.

Exports:AminoAcidContentAMIPCGRGC_contentOFDEGRSCU

Dependencies:ade4askpassBiocGenericsBiostringsclicolorspacecrayoncurlentropyfansifarverGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonlitekaoslabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangS4VectorsscalessegmentedseqinrspstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc