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:Michael Hahsler [aut, cre], Nagar Anurag [aut]

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'))

Peer review:

Bug tracker:https://github.com/mhahsler/rrdp/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:rRDP-1.39.0(bioc 3.20)rRDP-1.38.0(bioc 3.19)

geneticssequencinginfrastructureclassificationmicrobiomeimmunooncologyalignmentsequencematchingdataimportbayesianbioconductorbioinformatics

10 exports 1 stars 5.24 score 19 dependencies 3 scripts

Last updated 6 months agofrom:a5215a534e. Checks:OK: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 26 2024
R-4.5-winWARNINGSep 26 2024
R-4.5-linuxWARNINGSep 26 2024
R-4.4-winWARNINGSep 26 2024
R-4.4-macWARNINGSep 26 2024
R-4.3-winWARNINGSep 26 2024
R-4.3-macWARNINGSep 26 2024

Exports:accuracyconfusionTabledecode_Greengenesdecode_RDPencode_Greengenesencode_RDPGenClass16SrdpremoveRDPtrainRDP

Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6rJavaS4VectorssysUCSC.utilsXVectorzlibbioc

rRDP: Interface to the RDP Classifier

Rendered fromrRDP.Rmdusingknitr::rmarkdownon Sep 26 2024.

Last update: 2024-03-28
Started: 2024-03-26

Readme and manuals

Help Manual

Help pageTopics
Calculate Classification Accuracyaccuracy confusionTable
Decoding and Encoding Phylogenetic Classification Annotationsclassification decode_Greengenes decode_RDP encode_Greengenes encode_RDP GenClass16S
Ribosomal Database Project (RDP) Classifier for 16S rRNApredict predict.RDPClassifier print.RDPClassifier RDP rdp removeRDP trainRDP