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.
|Author||Andrew Hart [aut, cre], Servet Martnez [aut], Universidad de Chile [cph], INRIA-Chile [cph]|
|Maintainer||Andrew Hart <[email protected]>|
|License||GPL (>= 2)|
|Package repository||View on CRAN|
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