{
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  "Title": "Store and Transfer Amplicon Sequence Data",
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  "Date": "2026-10-16",
  "Authors@R": "c(\nperson(\"Sarah\", \"Westcott\", role = c(\"aut\"),\nemail = \"swestcot@umich.edu\",\ncomment = c(ORCID = \"0009-0001-1529-8247\")),\nperson(\"Gregory\", \"Johnson\", , \"grejoh@umich.edu\", role = c(\"aut\"),\ncomment = c(ORCID = \"0009-0008-3890-0297\")),\nperson(\"Pat\", \"Schloss\", , \"pschloss@umich.edu\",\nrole = c(\"cph\", \"cre\"), comment = c(ORCID = \"0000-0002-6935-4275\")))",
  "Maintainer": "Pat Schloss <pschloss@umich.edu>",
  "Description": "Stores the data associated with your amplicon sequence\nanalysis. This includes nucleotide sequences, abundance, sample\nand treatment assignments, taxonomic classifications, asv, otu\nand phylotype clusters, metadata, trees and various reports. It\nis designed to facilitate data analysis across multiple R\npackages with utility functions to read / write from 'mothur',\n'qiime2', 'dada2', and 'phyloseq'.",
  "URL": "https://github.com/mothur/strollur, https://mothur.org/strollur/",
  "BugReports": "https://github.com/mothur/strollur/issues",
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  "Repository": "https://mothur.r-universe.dev",
  "Date/Publication": "2026-10-16 15:16:38 UTC",
  "RemoteUrl": "https://github.com/mothur/strollur",
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  "Author": "Sarah Westcott [aut] (ORCID: <https://orcid.org/0009-0001-1529-8247>),\nGregory Johnson [aut] (ORCID: <https://orcid.org/0009-0008-3890-0297>),\nPat Schloss [cph, cre] (ORCID: <https://orcid.org/0000-0002-6935-4275>)",
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    "add",
    "assign",
    "clear",
    "copy_dataset",
    "count",
    "export_dataset",
    "get_bin_types",
    "has_sample",
    "has_sequence_strings",
    "import_dataset",
    "is_aligned",
    "is_equal",
    "load_dataset",
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    "names",
    "new_dataset",
    "new_reference",
    "read_biom",
    "read_dada2",
    "read_fasta",
    "read_fastq",
    "read_mothur",
    "read_mothur_cons_taxonomy",
    "read_mothur_count",
    "read_mothur_list",
    "read_mothur_oligos",
    "read_mothur_rabund",
    "read_mothur_shared",
    "read_mothur_taxonomy",
    "read_phyloseq",
    "read_qiime2",
    "read_qiime2_feature_table",
    "read_qiime2_metadata",
    "read_qiime2_taxonomy",
    "read_quality",
    "report",
    "save_dataset",
    "sort_dataframe",
    "strollur",
    "strollur_example",
    "summary",
    "unpack_qiime2_artifact",
    "write_biom",
    "write_fasta",
    "write_fastq",
    "write_mothur",
    "write_mothur_cons_taxonomy",
    "write_mothur_count",
    "write_mothur_design",
    "write_mothur_list",
    "write_mothur_rabund",
    "write_mothur_shared",
    "write_phyloseq",
    "write_quality",
    "write_taxonomy",
    "xdev_abundance",
    "xdev_add_references",
    "xdev_add_report",
    "xdev_add_sequence_fastq_scores",
    "xdev_add_sequences",
    "xdev_assign_bin_representative_sequences",
    "xdev_assign_bin_taxonomy",
    "xdev_assign_bin_taxonomy_tidy",
    "xdev_assign_bins",
    "xdev_assign_sample_distances",
    "xdev_assign_sequence_abundance",
    "xdev_assign_sequence_quality_scores",
    "xdev_assign_sequence_taxonomy",
    "xdev_assign_sequence_taxonomy_tidy",
    "xdev_assign_treatments",
    "xdev_count",
    "xdev_get_abundances_by_sample",
    "xdev_get_alignment_length",
    "xdev_get_bin_abundances_by_sample",
    "xdev_get_by_sample",
    "xdev_get_list_vector",
    "xdev_get_sample_distances",
    "xdev_get_sequence_abundances_by_sample",
    "xdev_get_sequence_indexes_by_sample",
    "xdev_get_sequences",
    "xdev_has_bin_taxonomy",
    "xdev_has_sequence_taxonomy",
    "xdev_merge_bins",
    "xdev_merge_sequences",
    "xdev_names",
    "xdev_remove_bins",
    "xdev_remove_lineages",
    "xdev_remove_samples",
    "xdev_remove_sequences",
    "xdev_report",
    "xdev_set_abundance",
    "xdev_set_abundances",
    "xdev_set_dataset_name",
    "xdev_set_sequences"
  ],
  "_help": [
    {
      "page": "abundance",
      "title": "Get the abundance data for sequences, bins, samples, and treatments in a strollur object",
      "topics": [
        "abundance"
      ]
    },
    {
      "page": "add",
      "title": "Add sequences, reports, trees or resource references to a strollur object",
      "topics": [
        "add"
      ]
    },
    {
      "page": "assign",
      "title": "Assign sequence abundances, sequence classifications, bins, bin representative sequences, bin classifications, sample distances or treatments to a strollur object",
      "topics": [
        "assign"
      ]
    },
    {
      "page": "clear",
      "title": "Clear data from a strollur object",
      "topics": [
        "clear"
      ]
    },
    {
      "page": "copy_dataset",
      "title": "Create a new strollur object from an existing dataset.",
      "topics": [
        "copy_dataset"
      ]
    },
    {
      "page": "count",
      "title": "Find the number of sequences, samples, treatments or bins of a given type in a strollur object",
      "topics": [
        "count"
      ]
    },
    {
      "page": "export_dataset",
      "title": "Create a human readable table containing all data from a strollur object.",
      "topics": [
        "export_dataset"
      ]
    },
    {
      "page": "get_bin_types",
      "title": "Get bin table types of a strollur object",
      "topics": [
        "get_bin_types"
      ]
    },
    {
      "page": "has_sample",
      "title": "Determine if a given sample is in a strollur object",
      "topics": [
        "has_sample"
      ]
    },
    {
      "page": "has_sequence_strings",
      "title": "Determine if a strollur object contains sequence nucleotide strings.",
      "topics": [
        "has_sequence_strings"
      ]
    },
    {
      "page": "import_dataset",
      "title": "Create a strollur object from the exported table of a strollur object",
      "topics": [
        "import_dataset"
      ]
    },
    {
      "page": "is_aligned",
      "title": "Determine if a strollur object contains aligned sequences.",
      "topics": [
        "is_aligned"
      ]
    },
    {
      "page": "is_equal",
      "title": "Determine if two strollur objects are equal.",
      "topics": [
        "is_equal"
      ]
    },
    {
      "page": "load_dataset",
      "title": "Load a strollur object from a file.",
      "topics": [
        "load_dataset"
      ]
    },
    {
      "page": "miseq_sop_example",
      "title": "Create a strollur object using the analysis files from the MiSeq_SOP example.",
      "topics": [
        "miseq_sop_example"
      ]
    },
    {
      "page": "names",
      "title": "Get the names of various data in a strollur object",
      "topics": [
        "names"
      ]
    },
    {
      "page": "new_dataset",
      "title": "Create a new strollur object",
      "topics": [
        "new_dataset"
      ]
    },
    {
      "page": "new_reference",
      "title": "Create a resource reference for your strollur object to aid in reproducibility.",
      "topics": [
        "new_reference"
      ]
    },
    {
      "page": "read_biom",
      "title": "Create a strollur object from a biom formatted file.",
      "topics": [
        "read_biom"
      ]
    },
    {
      "page": "read_dada2",
      "title": "Create a strollur object from dada2 outputs",
      "topics": [
        "read_dada2"
      ]
    },
    {
      "page": "read_fasta",
      "title": "Read a FASTA formatted sequence file",
      "topics": [
        "read_fasta"
      ]
    },
    {
      "page": "read_fastq",
      "title": "Read a FASTQ formatted file",
      "topics": [
        "read_fastq"
      ]
    },
    {
      "page": "read_mothur",
      "title": "Create a strollur object from mothur outputs",
      "topics": [
        "read_mothur"
      ]
    },
    {
      "page": "read_mothur_cons_taxonomy",
      "title": "Read a mothur formatted cons_taxonomy file",
      "topics": [
        "read_mothur_cons_taxonomy"
      ]
    },
    {
      "page": "read_mothur_count",
      "title": "Read a mothur formatted count file",
      "topics": [
        "read_mothur_count"
      ]
    },
    {
      "page": "read_mothur_list",
      "title": "Read a mothur formatted list file",
      "topics": [
        "read_mothur_list"
      ]
    },
    {
      "page": "read_mothur_oligos",
      "title": "Read a mothur formatted oligos file",
      "topics": [
        "read_mothur_oligos"
      ]
    },
    {
      "page": "read_mothur_rabund",
      "title": "Read a mothur formatted rabund file",
      "topics": [
        "read_mothur_rabund"
      ]
    },
    {
      "page": "read_mothur_shared",
      "title": "Read a mothur formatted shared file",
      "topics": [
        "read_mothur_shared"
      ]
    },
    {
      "page": "read_mothur_taxonomy",
      "title": "Read a mothur formatted taxonomy file",
      "topics": [
        "read_mothur_taxonomy"
      ]
    },
    {
      "page": "read_phyloseq",
      "title": "Create a strollur object from a phyloseq object",
      "topics": [
        "read_phyloseq"
      ]
    },
    {
      "page": "read_qiime2",
      "title": "Create a strollur object from a qiime2 outputs",
      "topics": [
        "read_qiime2"
      ]
    },
    {
      "page": "read_qiime2_feature_table",
      "title": "Read a qiime2 qza containing bin data",
      "topics": [
        "read_qiime2_feature_table"
      ]
    },
    {
      "page": "read_qiime2_metadata",
      "title": "Read a qiime2 .tsv table containing metadata.",
      "topics": [
        "read_qiime2_metadata"
      ]
    },
    {
      "page": "read_qiime2_taxonomy",
      "title": "Read a qiime2 qza containing taxonomy data",
      "topics": [
        "read_qiime2_taxonomy"
      ]
    },
    {
      "page": "read_quality",
      "title": "Read a file containing sequence quality scores",
      "topics": [
        "read_quality"
      ]
    },
    {
      "page": "remove_file",
      "title": "remove_file",
      "topics": [
        "remove_file"
      ]
    },
    {
      "page": "report",
      "title": "Get a data.frame containing the given report in a strollur object",
      "topics": [
        "report"
      ]
    },
    {
      "page": "save_dataset",
      "title": "Save the strollur object to file.",
      "topics": [
        "save_dataset"
      ]
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