spgs: 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.

Version: 1.0-1
Depends: R (≥ 3.0)
Imports: graphics, stats
Enhances: seqinr
Published: 2017-07-21
Author: Andrew Hart [aut, cre], Servet Martínez [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_1.0-1.tar.gz
Windows binaries: r-devel: spgs_1.0-1.zip, r-release: spgs_1.0-1.zip, r-oldrel: spgs_1.0-1.zip
OS X El Capitan binaries: r-release: spgs_1.0-1.tgz
OS X Mavericks binaries: r-oldrel: spgs_1.0-1.tgz
Old sources: spgs archive


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