Package: seq2R 2.0.1
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.zip(r-4.5)seq2R_2.0.1.zip(r-4.4)seq2R_2.0.1.zip(r-4.3)
seq2R_2.0.1.tgz(r-4.4-x86_64)seq2R_2.0.1.tgz(r-4.4-arm64)seq2R_2.0.1.tgz(r-4.3-x86_64)seq2R_2.0.1.tgz(r-4.3-arm64)
seq2R_2.0.1.tar.gz(r-4.5-noble)seq2R_2.0.1.tar.gz(r-4.4-noble)
seq2R.pdf |seq2R.html✨
seq2R/json (API)
| # Install 'seq2R' in R: |
| install.packages('seq2R', repos = c('https://noramvillanueva.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/noramvillanueva/seq2r/issues
- mtDNAhum - Human Mitochondrial DNA
bootstrapchange-pointsdna-sequencesgenome-analysismachine-learningnonparametric-statisticsregression
Last updated 2 months agofrom:1d21c297bf. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 03 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 03 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 03 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 03 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 03 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 03 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 03 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 03 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 03 2024 |
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 |
