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A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
| Version: | 1.0-4 |
| Depends: | R (≥ 3.0) |
| Imports: | graphics, stats |
| Enhances: | seqinr |
| Published: | 2023-10-03 |
| DOI: | 10.32614/CRAN.package.spgs |
| Author: | Andrew Hart [aut, cre], Servet MartÃnez [aut], Universidad de Chile [cph], INRIA-Chile [cph] |
| Maintainer: | Andrew Hart <ahart at dim.uchile.cl> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Copyright: | Universidad de Chile, INRIA-Chile |
| NeedsCompilation: | yes |
| Classification/MSC: | 62F03, 62G10, 62M07, 62P10, 92D20 |
| Citation: | spgs citation info |
| Materials: | NEWS |
| CRAN checks: | spgs results |
| Reference manual: | spgs.pdf |
| Package source: | spgs_1.0-4.tar.gz |
| Windows binaries: | r-devel: spgs_1.0-4.zip, r-release: spgs_1.0-4.zip, r-oldrel: spgs_1.0-4.zip |
| macOS binaries: | r-release (arm64): spgs_1.0-4.tgz, r-oldrel (arm64): spgs_1.0-4.tgz, r-release (x86_64): spgs_1.0-4.tgz, r-oldrel (x86_64): spgs_1.0-4.tgz |
| Old sources: | spgs archive |
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