Background | Starting Up | Read count files | Read distance matrix file | Clustering the data | Selecting different clustering methods | Output data from clustering
Package: clustur 0.1.4
Patrick Schloss
clustur: Clustering
A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) <doi:10.1128/AEM.01541-09>). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) <doi:10.1128/mspheredirect.00073-17>). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.
Authors:
clustur_0.1.4.tar.gz
clustur_0.1.4.zip(r-4.7)clustur_0.1.4.zip(r-4.6)clustur_0.1.4.zip(r-4.5)
clustur_0.1.4.tgz(r-4.6-x86_64)clustur_0.1.4.tgz(r-4.6-arm64)clustur_0.1.4.tgz(r-4.5-x86_64)clustur_0.1.4.tgz(r-4.5-arm64)
clustur_0.1.4.tar.gz(r-4.7-arm64)clustur_0.1.4.tar.gz(r-4.7-x86_64)clustur_0.1.4.tar.gz(r-4.6-arm64)clustur_0.1.4.tar.gz(r-4.6-x86_64)
clustur_0.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clustur/json (API)
| # Install 'clustur' in R: |
| install.packages('clustur', repos = c('https://schlosslab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/schlosslab/clustur/issues
Pkgdown/docs site:https://www.schlosslab.org
Last updated from:5d646f8894. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 277 | ||
| linux-devel-x86_64 | OK | 315 | ||
| source / vignettes | OK | 397 | ||
| linux-release-arm64 | OK | 284 | ||
| linux-release-x86_64 | OK | 294 | ||
| macos-release-arm64 | OK | 209 | ||
| macos-release-x86_64 | OK | 474 | ||
| macos-oldrel-arm64 | OK | 251 | ||
| macos-oldrel-x86_64 | OK | 426 | ||
| windows-devel | OK | 335 | ||
| windows-release | OK | 325 | ||
| windows-oldrel | OK | 285 | ||
| wasm-release | OK | 281 |
Exports:clustercreate_sparse_matrixexample_pathget_abundanceget_binsget_count_tableget_cutoffget_distance_dfget_metricsread_countread_distsplit_clusters_to_listvalidate_count_table
Dependencies:briocallrclicrayondescdiffobjevaluatefsgluejsonlitelatticelifecyclemagrittrMatrixotelpkgbuildpkgloadpraiseprocessxpsR6Rcpprlangrprojroottestthatwaldowithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cluster entities together | cluster |
| Create Sparse Matrix | create_sparse_matrix |
| Example Path | example_path |
| Get Shared | get_abundance |
| Get Clusters | get_bins |
| Get Count Table | get_count_table |
| Get Cutoff | get_cutoff |
| Get Distance Data Frame | get_distance_df |
| Get Metrics | get_metrics |
| Read count table | read_count |
| Read distance matrices | read_dist |
| Split Clusters to List | split_clusters_to_list |
| Validate Count Table | validate_count_table |
