In mhahsler/rRDP: Interface to the RDP Classifier

pkg <- "rRDP"

source("https://raw.githubusercontent.com/mhahsler/pkg_helpers/main/pkg_helpers.R")
pkg_title(pkg, CRAN = FALSE, Bioc = TRUE)

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.

Other R interfaces for bioinformatics are also available:

• rBLAST: Interface to the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases
• rMSA: Interface for Popular Multiple Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE, and Kalign

Installation

if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("rRDP")
BiocManager::install("rRDPData")

Usage

library(rRDP)

Load a few sequences and classify the sequences using RDP.

seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
  package="rRDP"))
seq

pred <- predict(rdp(), seq)
pred

attr(pred, "confidence")

Citation Request

pkg_citation(pkg)

Acknowledgments

This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

mhahsler/rRDP documentation built on April 29, 2024, 9:11 a.m.