Package: ClassifyITS
Title: Fungal Assignment Pipeline
Version: 1.0.2
Authors@R: person("Quinn Moon", email = "qmoon@umich.edu", role = c("aut", "cre"))
Description: Fungi are ubiquitous in Earth's wonderfully diverse ecosystems. The 'ClassifyITS' package aids in the taxonomic classification of environmental internal transcribed spacer (ITS) short-read barcoding data. Unlike previous methods, it employs taxon-specific e-value and percent identity cutoffs at each taxonomic rank from kingdom to species. The package takes a conservative approach and outputs both graphics and user-friendly files to help users manually inspect fungal operational taxonomic units (OTUs) that fail classification at relevant levels (e.g., Phylum). 'ClassifyITS' is based on taxonomic cutoff criteria from "The Global Soil Mycobiome consortium dataset for boosting fungal diversity research" (Fungal Diversity, Tedersoo, 2021, <doi:10.1007/s13225-021-00493-7>) and "Best practices in metabarcoding of fungi: From experimental design to results" (Molecular Ecology, Tedersoo, 2022, <doi:10.1111/mec.16460>).
License: GPL-3
Encoding: UTF-8
Imports: ggplot2, gridExtra, grid, reshape2, data.table, seqinr
Suggests: formatR, knitr, rmarkdown
RoxygenNote: 7.3.3
VignetteBuilder: knitr, rmarkdown, formatR
NeedsCompilation: no
Packaged: 2026-04-23 15:11:19 UTC; quinnmoon
Author: Quinn Moon [aut, cre]
Maintainer: Quinn Moon <qmoon@umich.edu>
Repository: CRAN
Date/Publication: 2026-04-23 15:40:02 UTC
Built: R 4.6.0; ; 2026-04-28 00:45:59 UTC; unix
