Package: rRDP 1.37.3
rRDP: Interface to the RDP Classifier
This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained.
Authors:
rRDP_1.37.3.tar.gz
rRDP_1.37.3.zip(r-4.5)rRDP_1.37.3.zip(r-4.4)rRDP_1.37.3.zip(r-4.3)
rRDP_1.37.3.tgz(r-4.4-any)rRDP_1.37.3.tgz(r-4.3-any)
rRDP_1.37.3.tar.gz(r-4.5-noble)rRDP_1.37.3.tar.gz(r-4.4-noble)
rRDP_1.37.3.tgz(r-4.4-emscripten)rRDP_1.37.3.tgz(r-4.3-emscripten)
rRDP.pdf |rRDP.html✨
rRDP/json (API)
NEWS
| # Install 'rRDP' in R: |
| install.packages('rRDP', repos = c('https://mhahsler.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mhahsler/rrdp/issues
On BioConductor:rRDP-1.41.0(bioc 3.21)rRDP-1.40.0(bioc 3.20)
geneticssequencinginfrastructureclassificationmicrobiomeimmunooncologyalignmentsequencematchingdataimportbayesianbioconductorbioinformaticsopenjdk
Last updated 8 months agofrom:a5215a534e. Checks:OK: 1 WARNING: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 25 2024 |
| R-4.5-win | WARNING | Nov 25 2024 |
| R-4.5-linux | WARNING | Nov 25 2024 |
| R-4.4-win | WARNING | Nov 25 2024 |
| R-4.4-mac | WARNING | Nov 25 2024 |
| R-4.3-win | WARNING | Nov 25 2024 |
| R-4.3-mac | WARNING | Nov 25 2024 |
Exports:accuracyconfusionTabledecode_Greengenesdecode_RDPencode_Greengenesencode_RDPGenClass16SrdpremoveRDPtrainRDP
Dependencies:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6rJavaS4VectorssysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Classification Accuracy | accuracy confusionTable |
| Decoding and Encoding Phylogenetic Classification Annotations | classification decode_Greengenes decode_RDP encode_Greengenes encode_RDP GenClass16S |
| Ribosomal Database Project (RDP) Classifier for 16S rRNA | predict predict.RDPClassifier print.RDPClassifier RDP rdp removeRDP trainRDP |
