{ "_id": "6ad88a68d556c3a3418a89d8", "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\necosystems. The 'ClassifyITS' package aids in the taxonomic\nclassification of internal transcribed spacer (ITS) fungal\nsequences. Unlike previous methods, it employs taxon-specific\ne-value and percent identity cutoffs at each taxonomic rank\nfrom kingdom to species. The package takes a conservative\napproach and outputs both graphics and user-friendly files to\nhelp users manually inspect fungal operational taxonomic units\n(OTUs) that fail classification at relevant levels (e.g.,\nPhylum). 'ClassifyITS' is based on taxonomic cutoff criteria\nfrom \"The Global Soil Mycobiome consortium dataset for boosting\nfungal diversity research\" (Fungal Diversity, Tedersoo, 2021,\n) and \"Best practices in\nmetabarcoding of fungi: From experimental design to results\"\n(Molecular Ecology, Tedersoo, 2022, ).", "License": "GPL-3", "Encoding": "UTF-8", "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": { "Date": "2026-10-21 09:44:41 UTC", "User": "root" }, "Author": "Quinn Moon [aut, cre]", "Maintainer": "Quinn Moon ", "_user": "qmoon11", "_type": "src", "_file": "ClassifyITS_1.0.3.tar.gz", "_fileid": 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"trim_alignments", "write_initial_assignments" ], "_help": [ { "page": "best_hit_taxonomy_assignment", "title": "Hierarchical best-hit taxonomy assignment with per-rank fallback rule", "topics": [ "best_hit_taxonomy_assignment" ] }, { "page": "check_N", "title": "Check proportion of N bases in each sequence.", "topics": [ "check_N" ] }, { "page": "consensus_taxonomy_assignment", "title": "Per-rank consensus filter for taxonomy assignment", "topics": [ "consensus_taxonomy_assignment" ] }, { "page": "easy_assignments", "title": "Easy taxonomy assignment for OTUs using BLAST QC output & phylum-specific thresholds.", "topics": [ "easy_assignments" ] }, { "page": "ensure_cols", "title": "Ensure data frame has all required columns (as character)", "topics": [ "ensure_cols" ] }, { "page": "ITS_assignment", "title": "Complete Fungal Assignment Pipeline", "topics": [ "ITS_assignment" ] }, { "page": "load_and_check", "title": "Load and check BLAST results and rep-seq FASTA", "topics": [ "load_and_check" ] }, { "page": "parse_taxonomy_cutoffs", "title": "Parse taxonomy cutoffs file", "topics": [ "parse_taxonomy_cutoffs" ] }, { "page": "plot_alignment_hist", "title": "Create and return alignment length histogram (ggplot object)", "topics": [ "plot_alignment_hist" ] }, { "page": "safe_rbind_list", "title": "Safely rbinds list of data frames, ensuring columns match", "topics": [ "safe_rbind_list" ] }, { "page": "save_taxonomy_graphics", "title": "Save taxonomy summary charts and tables to multi-page PDF", "topics": [ "save_taxonomy_graphics" ] }, { "page": "trim_alignments", "title": "Trim BLAST alignments by minimum length", "topics": [ "trim_alignments" ] }, { "page": "write_initial_assignments", "title": "Create and write the initial assignments table including drops at all steps", "topics": [ "write_initial_assignments" ] } ], "_readme": "https://github.com/qmoon11/classifyits/raw/HEAD/README.md", "_rundeps": [ "ade4", "cli", "cpp11", "data.table", "farver", 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