Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018)
insect is an R package for DNA meta-barcoding analysis. It provides a
bioinformatics pipeline that automates the process from HTS sequence
de-multiplexing and quality filtering to probabilistic taxonomic
assignment using informatic sequence classification trees.
It also contains functions for searching and downloading sequences
from GenBank, a "virtual PCR" tool, a new algorithm for classification tree learning,
and a method for classifying DNA barcode sequences using pre-computed trees.
To download insect from CRAN and load the package, run
install.packages("insect")library(insect)To download the latest development version from GitHub, run:
devtools::install_github("shaunpwilkinson/insect", build_vignettes = TRUE) library("insect")An overview of the package and its functions can be found by running
vignette("insect-vignette")If you experience a problem using this package please feel free to raise it as an issue on GitHub.
This software was developed at Victoria University of Wellington with funding from a Rutherford Foundation Postdoctoral Research Fellowship award from the Royal Society of New Zealand.