Getting started with | Building the database | Classifying a single unkown sequence | Classifying multiple unknown sequences | Classifying multiple unknown sequences in parallel | Run-to-run variation | Alternative databases
Package: phylotypr 0.1.1
Pat Schloss
phylotypr: Classifying DNA Sequences to Taxonomic Groupings
Classification based analysis of DNA sequences to taxonomic groupings. This package primarily implements Naive Bayesian Classifier from the Ribosomal Database Project. This approach has traditionally been used to classify 16S rRNA gene sequences to bacterial taxonomic outlines; however, it can be used for any type of gene sequence. The method was originally described by Wang, Garrity, Tiedje, and Cole in Applied and Environmental Microbiology 73(16):5261-7 <doi:10.1128/AEM.00062-07>. The package also provides functions to read in 'FASTA'-formatted sequence data.
Authors:
phylotypr_0.1.1.tar.gz
phylotypr_0.1.1.zip(r-4.7-x86_64)phylotypr_0.1.1.zip(r-4.7-arm64)phylotypr_0.1.1.zip(r-4.6-x86_64)phylotypr_0.1.1.zip(r-4.6-arm64)phylotypr_0.1.1.zip(r-4.5-x86_64)
phylotypr_0.1.1.tgz(r-4.6-x86_64)phylotypr_0.1.1.tgz(r-4.6-arm64)phylotypr_0.1.1.tgz(r-4.5-x86_64)phylotypr_0.1.1.tgz(r-4.5-arm64)
phylotypr_0.1.1.tar.gz(r-4.7-arm64)phylotypr_0.1.1.tar.gz(r-4.7-x86_64)phylotypr_0.1.1.tar.gz(r-4.6-arm64)phylotypr_0.1.1.tar.gz(r-4.6-x86_64)
phylotypr_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylotypr/json (API)
| # Install 'phylotypr' in R: |
| install.packages('phylotypr', repos = c('https://mothur.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mothur/phylotypr/issues
Pkgdown/docs site:https://mothur.org
Datasets:
- trainset9_pds - RDP training set v9
- trainset9_rdp - RDP training set v9
Last updated from:ce15101332. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 108 | ||
| linux-devel-x86_64 | OK | 145 | ||
| source / vignettes | OK | 254 | ||
| linux-release-arm64 | OK | 110 | ||
| linux-release-x86_64 | OK | 143 | ||
| macos-release-arm64 | OK | 161 | ||
| macos-release-x86_64 | OK | 197 | ||
| macos-oldrel-arm64 | OK | 164 | ||
| macos-oldrel-x86_64 | OK | 306 | ||
| windows-devel-arm64 | OK | 238 | ||
| windows-devel-x86_64 | OK | 165 | ||
| windows-release-arm64 | OK | 220 | ||
| windows-release-x86_64 | OK | 116 | ||
| windows-oldrel-x86_64 | OK | 118 | ||
| wasm-release | OK | 114 |
Exports:build_kmer_databaseclassify_sequencefilter_taxonomyphylotypr_exampleprint_taxonomyread_fastaread_taxonomywrite_fasta
Dependencies:bitbit64clicliprcpp11crayongluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6Rcppreadrrlangstringitibbletidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build kmer database | build_kmer_database |
| Classify 16S rRNA gene sequence fragment | classify_sequence |
| Filter taxonomy | filter_taxonomy |
| Get path to phylotypr example | phylotypr_example |
| Print taxonomy for an unknown sequence | print_taxonomy |
| Read in a FASTA-formatted file containing DNA sequences | read_fasta |
| Read in taxonomy files | read_taxonomy |
| RDP training set v9 | trainset9_pds trainset9_rdp |
| Write to a FASTA-formatted file | write_fasta |