Introduction | Input files | Reading the input | Classification of a single sequence
Package: clstutils 1.61.0
Noah Hoffman
clstutils: Tools for performing taxonomic assignment
Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.
Authors:
clstutils_1.61.0.tar.gz
clstutils_1.61.0.zip(r-4.7)clstutils_1.61.0.zip(r-4.6)clstutils_1.61.0.zip(r-4.5)
clstutils_1.61.0.tgz(r-4.6-any)clstutils_1.61.0.tgz(r-4.5-any)
clstutils_1.61.0.tar.gz(r-4.7-any)clstutils_1.61.0.tar.gz(r-4.6-any)
clstutils_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
clstutils/json (API)
| # Install 'clstutils' in R: |
| install.packages('clstutils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:clstutils-1.61.0(bioc 3.24)clstutils-1.60.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingclassificationvisualizationqualitycontrol
Last updated from:0dd3a03110. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 134 | ||
| linux-devel-x86_64 | WARNING | 159 | ||
| source / vignettes | OK | 156 | ||
| linux-release-x86_64 | WARNING | 185 | ||
| macos-release-arm64 | WARNING | 96 | ||
| macos-oldrel-arm64 | WARNING | 130 | ||
| windows-devel | WARNING | 112 | ||
| windows-release | WARNING | 121 | ||
| windows-oldrel | WARNING | 89 | ||
| wasm-release | OK | 143 |
Exports:classifyPlacementsfindOutliersmaxDistsprettyTreerefpkgContentstaxonomyFromRefpkgtreeDists
Dependencies:apebitbit64blobcachemcliclstcpp11DBIdigestevaluatefastmapgluehighrknitrlatticelifecyclememoisenlmepkgconfigRcpprjsonrlangROCRSQLitevctrsxfunyaml
clst
Last update: 2019-12-23
Started: 2013-11-01
clstutils
Introduction | Finding outliers | Selecting a diverse subset
Last update: 2019-12-23
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Sequence based classification and selection of reference sequences. | clstutils-package clstutils |
| Taxonomic classification by phylogenetic placement. | classifyPlacements |
| Identify outlier objects given a square distance matrix. | findOutliers |
| Select a maximally diverse set of items given a distance matrix. | maxDists |
| Draw an annotated phylogenetic tree. | prettyTree |
| Read the contents of a collection of reference sequences ("refpkg"). | refpkgContents |
| Annotation for the Enterococcus sequence data set. | seqdat |
| Enterococcus sequence data set. | seqs |
| Extract taxonomic information from a refpkg. | taxonomyFromRefpkg |
| Provide objects for determining distances among nodes of a reference tree. | treeDists |
