Introduction | Distance matrix computation | Example 1: Compute k-mer distance matrices for the woodmouse dataset | Example 2: Alignment-free tree-building | Acknowledgements | References
Package: kmer 1.1.3
kmer: Fast K-Mer Counting and Clustering for Biological Sequence Analysis
Contains tools for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning. See Vinga and Almeida (2003) <doi:10.1093/bioinformatics/btg005> for a review of k-mer counting methods and applications for biological sequence analysis.
Authors:
kmer_1.1.3.tar.gz
kmer_1.1.3.zip(r-4.7)kmer_1.1.3.zip(r-4.6)kmer_1.1.3.zip(r-4.5)
kmer_1.1.3.tgz(r-4.6-x86_64)kmer_1.1.3.tgz(r-4.6-arm64)kmer_1.1.3.tgz(r-4.5-x86_64)kmer_1.1.3.tgz(r-4.5-arm64)
kmer_1.1.3.tar.gz(r-4.7-arm64)kmer_1.1.3.tar.gz(r-4.7-x86_64)kmer_1.1.3.tar.gz(r-4.6-arm64)kmer_1.1.3.tar.gz(r-4.6-x86_64)
kmer_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
kmer/json (API)
| # Install 'kmer' in R: |
| install.packages('kmer', repos = c('https://shaunpwilkinson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/shaunpwilkinson/kmer/issues
Last updated from:1b28b44796. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 147 | ||
| linux-devel-x86_64 | OK | 134 | ||
| source / vignettes | OK | 200 | ||
| linux-release-arm64 | OK | 136 | ||
| linux-release-x86_64 | OK | 137 | ||
| macos-release-arm64 | OK | 82 | ||
| macos-release-x86_64 | OK | 259 | ||
| macos-oldrel-arm64 | OK | 78 | ||
| macos-oldrel-x86_64 | OK | 296 | ||
| windows-devel | OK | 136 | ||
| windows-release | OK | 114 | ||
| windows-oldrel | OK | 129 | ||
| wasm-release | OK | 137 |
Exports:clusterkcountkdistancembedotu
Dependencies:apeaskpassdigestlatticenlmeopensslphylogramRcppsys
