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:	1.0-4
Depends:	R (≥ 3.0)
Imports:	graphics, stats
Enhances:	seqinr
Published:	2023-10-03
DOI:	10.32614/CRAN.package.spgs
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

Documentation:

Reference manual:

spgs.html , spgs.pdf

Downloads:

Package source:	spgs_1.0-4.tar.gz
Windows binaries:	r-devel: spgs_1.0-4.zip, r-release: spgs_1.0-4.zip, r-oldrel: spgs_1.0-4.zip
macOS binaries:	r-release (arm64): spgs_1.0-4.tgz, r-oldrel (arm64): spgs_1.0-4.tgz, r-release (x86_64): spgs_1.0-4.tgz, r-oldrel (x86_64): spgs_1.0-4.tgz
Old sources:	spgs archive

Reverse dependencies:

Reverse suggests:

prmisc

Linking:

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