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ClassifyITS  

Fungal Assignment Pipeline
View on CRAN: Click here


Download and install ClassifyITS package within the R console
Install from CRAN:
install.packages("ClassifyITS")

Install from Github:
library("remotes")
install_github("cran/ClassifyITS")

Install by package version:
library("remotes")
install_version("ClassifyITS", "1.0.3")



Attach the package and use:
library("ClassifyITS")
Maintained by
Quinn Moon
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-04-09
Latest Update: 2026-04-09
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>).
How to cite:
Quinn Moon (2026). ClassifyITS: Fungal Assignment Pipeline. R package version 1.0.3, https://cran.r-project.org/web/packages/ClassifyITS. Accessed 30 Oct. 2026.
Previous versions and publish date:
0.1.0 (2026-04-09 17:20), 1.0.2 (2026-04-23 17:40), (2026-08-26 01:20)
Other packages that cited ClassifyITS R package
View ClassifyITS citation profile
Other R packages that ClassifyITS depends, imports, suggests or enhances
Complete documentation for ClassifyITS
Functions, R codes and Examples using the ClassifyITS R package
Full ClassifyITS package functions and examples
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