README.md

insect

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Informatic sequence classification trees

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.

Installation

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")

Help

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.

Acknowledgements

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.



shaunpwilkinson/insect documentation built on Aug. 18, 2018, 10:08 a.m.