{ "_id": "6a1866efacfb0bcc41dc057c", "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\necosystems. The 'ClassifyITS' package aids in the taxonomic\nclassification of environmental internal transcribed spacer\n(ITS) short-read barcoding data. Unlike previous methods, it\nemploys taxon-specific e-value and percent identity cutoffs at\neach taxonomic rank from kingdom to species. The package takes\na conservative approach and outputs both graphics and\nuser-friendly files to help users manually inspect fungal\noperational taxonomic units (OTUs) that fail classification at\nrelevant levels (e.g., Phylum). 'ClassifyITS' is based on\ntaxonomic cutoff criteria from \"The Global Soil Mycobiome\nconsortium dataset for boosting fungal diversity research\"\n(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", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr, rmarkdown, formatR", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://qmoon11.r-universe.dev", "Date/Publication": "2026-05-28 13:48:14 UTC", "RemoteUrl": "https://github.com/qmoon11/classifyits", "RemoteRef": "HEAD", "RemoteSha": "36f37f83624a2ded9608943381ae7964feff453a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 15:10:37 UTC", "User": "root" }, "Author": "Quinn Moon [aut, cre]", "Maintainer": "Quinn Moon ", "MD5sum": "26faaed2667824f5b737725042a5d896", "_user": "qmoon11", "_type": "src", "_file": "ClassifyITS_1.0.2.tar.gz", "_fileid": 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"Imports" }, { "package": "grid", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "formatR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "qmoon11", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-07", "n": 12 }, { "week": "2026-08", "n": 14 }, { "week": "2026-13", "n": 6 }, { "week": "2026-14", "n": 4 }, { "week": "2026-17", "n": 11 }, { "week": "2026-22", "n": 2 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "qmoon11", "count": 23, "uuid": 161752423 } ], "_userbio": { "uuid": 161752423, "type": "user", "name": "Quinn Moon", "description": "Fungal curious for sure" }, "_downloads": { "count": 490, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ClassifyITS" }, "_devurl": "https://github.com/qmoon11/classifyits", "_searchresults": 5, 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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", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pixmap", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S7", "scales", "segmented", "seqinr", "sp", "stringi", 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