[aut, cre]Contains tools to calculate similarity score matrix for DNA k-mers. The pairwise similarity score is calculated using PAM or BLOSUM substitution matrix. The results are evaluated by similarity score calculated by Needleman-Wunsch (1970) <doi:10.1016/0022-2836(70)90057-4> global or Smith-Waterman (1981) <doi:10.1016/0022-2836(81)90087-5> local alignment. Higher similarity score indicates more similar sequences for BLOSUM and less similar sequences for PAM matrix; 30, 40, 70, 120, 250 and 62, 45, 50, 62, 80, 100 matrix versions are available for PAM and BLOSUM, respectively.
| Version: | 1.1.0 |
| Depends: | R (≥ 3.4.0) |
| Imports: | tcR, rDNAse, utils, stats, Biostrings |
| Suggests: | knitr, ape (≥ 4.0), rmarkdown |
| Published: | 2018-11-03 |
| Author: | Rafal Urniaz
[aut, cre] |
| Maintainer: | Rafal Urniaz <rafal.urniaz at gmail.com> |
| BugReports: | http://github.com/RafalUrniaz/kmeRs/issues |
| License: | GPL-3 |
| URL: | https://rafalurniaz.github.io/kmeRs/ |
| NeedsCompilation: | no |
| Citation: | kmeRs citation info |
| CRAN checks: | kmeRs results |
| Reference manual: | kmeRs.pdf |
| Vignettes: |
Introduction to the kmeRs R package |
| Package source: | kmeRs_1.1.0.tar.gz |
| Windows binaries: | r-devel: kmeRs_1.1.0.zip, r-release: kmeRs_1.1.0.zip, r-oldrel: kmeRs_1.1.0.zip |
| macOS binaries: | r-release: kmeRs_1.1.0.tgz, r-oldrel: kmeRs_1.1.0.tgz |
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