{ "_id": "6a33d33c3efcd9bda43b45c9", "Package": "demulticoder", "Title": "Simultaneous Analysis of Multiplexed Metabarcodes", "Version": "0.1.2", "Authors@R": "c(person(\"Martha A.\", \"Sudermann\", email = \"sudermam@oregonstate.edu\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Zachary S. L\", \"Foster\", role = \"aut\"), person(\"Samantha\", \"Dawson\", role = \"aut\"), person(\"Hung\", \"Phan\", role = \"aut\"), person(\"Jeff\", \"H. Chang\", role = \"aut\"), person(\"Niklaus\", \"Grünwald\", role = c(\"aut\", \"cph\")))", "Description": "A comprehensive set of wrapper functions for the analysis\nof multiplex metabarcode data. It includes robust wrappers for\n'Cutadapt' and 'DADA2' to trim primers, filter reads, perform\namplicon sequence variant (ASV) inference, and assign taxonomy.\nThe package can handle single metabarcode datasets, datasets\nwith two pooled metabarcodes, or multiple datasets\nsimultaneously. The final output is a matrix per metabarcode,\ncontaining both ASV abundance data and associated taxonomic\nassignments. An optional function converts these matrices into\n'phyloseq' and 'taxmap' objects. For more information on\n'DADA2', including information on how 'DADA2' infers samples\nsequences, see Callahan et al. (2016) .\nFor more details on the 'demulticoder' R package see Sudermann\net al. (2025) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "URL": "https://grunwaldlab.github.io/demulticoder/,\nhttps://github.com/grunwaldlab/demulticoder", "BugReports": "https://github.com/grunwaldlab/demulticoder/issues", "RoxygenNote": "7.3.2", "Config/Needs/website": "rmarkdown", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 11:11:11 UTC", "User": "root" }, "Maintainer": "Martha A. Sudermann ", "Config/pak/sysreqs": "libicu-dev libx11-dev", "Repository": "https://grunwaldlab.r-universe.dev", "Date/Publication": "2025-06-13 18:38:48 UTC", "RemoteUrl": "https://github.com/grunwaldlab/demulticoder", "RemoteRef": "HEAD", "RemoteSha": "1b828f933bee26b0c76497809f172af472e61939", "Author": "Martha A. Sudermann [aut, cre, cph],\nZachary S. L Foster [aut],\nSamantha Dawson [aut],\nHung Phan [aut],\nJeff H. 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Sudermann", "email": "sudermam@oregonstate.edu", "login": "masudermann", "description": "Postdoc in Chang and Grunwald Labs", "uuid": 89535005 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.2", "role": "Depends" }, { "package": "furrr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "Biostrings", "role": "Suggests" }, { "package": "dada2", "role": "Suggests" }, { "package": "metacoder", "role": "Suggests" }, { "package": "ShortRead", "role": "Suggests" }, { "package": "phyloseq", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": 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