Package: ClassifyITS
Title: Fungal Assignment Pipeline
Version: 1.0.3
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 internal transcribed spacer (ITS) fungal
        sequences. 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
VignetteBuilder: knitr, rmarkdown, formatR
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://qmoon11.r-universe.dev
Date/Publication: 2026-08-25 20:43:09 UTC
RemoteUrl: https://github.com/qmoon11/classifyits
RemoteRef: HEAD
RemoteSha: 865a279881cc9172b0493860541a791f36d402b6
NeedsCompilation: no
Packaged: 2026-10-21 09:44:41 UTC; root
Author: Quinn Moon [aut, cre]
Maintainer: Quinn Moon <qmoon@umich.edu>