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spgs
View on CRAN: Click
here
Download and install spgs package within the R console
Install from CRAN:
install.packages("spgs")
Install from Github:
library("remotes")
install_github("cran/spgs") Install by package version:
library("remotes")
install_version("spgs", "1.0-4") Attach the package and use:
library("spgs")
Maintained by
Andrew Hart
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-03-28
Latest Update: 2023-10-03
Description:
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.
How to cite:
Andrew Hart (2015). spgs: Statistical Patterns in Genomic Sequences. R package version 1.0-4, https://cran.r-project.org/web/packages/spgs. Accessed 07 Oct. 2026.
Previous versions and publish date:
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Other R packages that spgs depends,
imports, suggests or enhances
Complete documentation for spgs
Functions, R codes and Examples using
the spgs R package
Some associated functions: ag.test . agct.test . array2vector . chargaff.gibbs.test . chargaff0.test . chargaff1.test . chargaff2.test . chisq.unif.test . complement . cylinder.counts . diffsign.test . diid.disturbance . diid.test . disambiguate . estimateMarkovChain . ks.unif.test . lb.test . markov.disturbance . markov.test . nanoarchaeum . oligoProfile . pair.counts . pieris . quadruple.counts . rank.test . rcspr2mat . reverseComplement . rstochmat . rstochvec . simulateMarkovChain . spgs-package . triple.counts . turningpoint.test .
Some associated R codes: FHatCovariances.R . GibbsCovariances.R . ISPHelpers.R . MarkovChains.R . ag.test.R . agct.test.R . auxtests.R . chargaff.gibbs.test.R . chargaff0.test.R . chargaff1.test.R . chargaff2.test.R . complement.R . counting.R . diid.test.R . disambiguate.R . hooks.R . markov.test.R . oligoCorr.R . print.R . profile.R . randmat.R . reverseComplement.R . Full spgs package functions and examples
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