Statistical Patterns in Genomic Sequences

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.


Reference manual

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install.packages("spgs")

1.0-4 by Andrew Hart, 3 years ago


Browse source code at https://github.com/cran/spgs


Authors: Andrew Hart [aut, cre] , Servet Martínez [aut] , Universidad de Chile [cph] , INRIA-Chile [cph]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports graphics, stats

Enhances seqinr


Suggested by prmisc.


See at CRAN