Simple Method to Detect Compositional Changes in Genomic Sequences
This software is useful for loading '.fasta' or '.gbk' files, and for retrieving sequences from 'GenBank' dataset https://www.ncbi.nlm.nih.gov/genbank/. This package allows to detect differences or asymmetries based on nucleotide composition by using local linear kernel smoothers. Also, it is possible to draw inference about critical points (i. e. maximum or minimum points) related with the derivative curves. Additionally, bootstrap methods have been used for estimating confidence intervals and speed computational techniques (binning techniques) have been implemented in 'seq2R'.
The full methodology of the method to detect changes points in DNA sequences is published in the following paper:
Villanueva, N.M., Sestelo, M., Fonseca, M.M. & Roca-Pardinas, J. seq2R: an R package to detect change points in DNA sequences. Mathematics 11, pages 2299 (2023). https://doi.org/10.3390/math11102299
seq2R is available through both CRAN and Github
If you want to use the release version of the package, you can install the package from CRAN as follows:
install.packages(pkgs="seq2R");
Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("noramvillanueva/seq2R")
@article{villanueva2023,
author = {Villanueva, Nora M. and Sestelo, Marta, Fonseca, Miguel M. and Roca-Pardinas, Javier},
doi = {10.3390/math11102299},
issn = {2227-7390},
journal = {Mathematics},
number = {10},
pages = {6},
title = {{seq2R: An R Package to Detect Change Points in DNA Sequences}},
url = {https://doi.org/10.3390/math11102299},
volume = {11},
year = {2023}
}