Package: seq2R 2.0.1
Nora M. Villanueva
seq2R: 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'.
Authors:
seq2R_2.0.1.tar.gz
seq2R_2.0.1.tar.gz(r-4.5-noble)seq2R_2.0.1.tar.gz(r-4.4-noble)
seq2R_2.0.1.tgz(r-4.4-emscripten)
seq2R.pdf |seq2R.html✨
seq2R/json (API)
| # Install 'seq2R' in R: |
| install.packages('seq2R', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- mtDNAhum - Human Mitochondrial DNA
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 months agofrom:60532b8dc3. Checks:2 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-linux-x86_64 | OK | Feb 28 2025 |
Exports:criticalfind.pointsplot.change.pointsprint.change.pointsread.allread.genbanktransform
Dependencies:ade4latticeMASSnlmepixmapRcppRcppArmadillosegmentedseqinrsp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simple method to detect compositional changes in genomic sequences | seq2R-package seq2R |
| Critical points (maxima and minima) | critical |
| Simple method to detect compositional changes in genomic sequences | find.points |
| Human Mitochondrial DNA | mtDNAhum |
| Visualization of change.points objects | plot.change.points |
| Short find.points summary | print.change.points |
| Read FASTA and GBK formatted files | read.all |
| Read DNA sequences from GenBank via internet | read.genbank |
| Convert biological sequences into binary code | transform |
