Informatic Sequence Classification Trees

Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) .


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.

News

Reference manual

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install.packages("insect")

1.2.0 by Shaun Wilkinson, 15 days ago


http://github.com/shaunpwilkinson/insect


Report a bug at http://github.com/shaunpwilkinson/insect/issues


Browse source code at https://github.com/cran/insect


Authors: Shaun Wilkinson [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports ape, aphid, kmer, openssl, phylogram, RANN, seqinr, stats, utils, xml2

Suggests knitr, rmarkdown, testthat


See at CRAN