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 purinepyrimidine 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 firstorder Markovianness. Also, it has functions for counting words/kmers (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.
Package details 


Author  Andrew Hart [aut, cre], Servet Martnez [aut], Universidad de Chile [cph], INRIAChile [cph] 
Maintainer  Andrew Hart <[email protected]> 
License  GPL (>= 2) 
Version  1.02 
Package repository  View on CRAN 
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