Statistical Patterns in Genomic Sequences
R package spgs version 1.0-4
Classification/MSC: 62F03, 62G10, 62M07, 62P10, 92D20
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.
Software
Depends: R (>= 3.0)
Imports: graphics, stats
Enhances: seqinr
Andrew Hart <ahart@dim.uchile.cl>
Comprehensive R Archive Network (CRAN)
Andrew Hart [aut, cre],
Servet MartÃnez [aut],
Universidad de Chile [cph],
INRIA-Chile [cph]
GPL (>= 2)
2023-10-03
application/tgz
https://CRAN.R-project.org/package=spgs
doi:10.32614/CRAN.package.spgs