{
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  "Package": "memes",
  "Type": "Package",
  "Title": "motif matching, comparison, and de novo discovery using the MEME\nSuite",
  "Version": "1.21.0",
  "Authors@R": "person(\"Spencer\", \"Nystrom\",\nemail = \"nystromdev@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-1000-1579\"))",
  "Description": "A seamless interface to the MEME Suite family of tools for\nmotif analysis. 'memes' provides data aware utilities for using\nGRanges objects as entrypoints to motif analysis, data\nstructures for examining & editing motif lists, and novel data\nvisualizations. 'memes' functions and data structures are\namenable to both base R and tidyverse workflows.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "biocViews": "DataImport, FunctionalGenomics, GeneRegulation,\nMotifAnnotation, MotifDiscovery, SequenceMatching, Software",
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  "BugReports": "https://github.com/snystrom/memes/issues",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake git make libgit2-dev libicu-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:24 UTC",
  "RemoteUrl": "https://github.com/bioc/memes",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:44:23 UTC",
    "User": "root"
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  "Author": "Spencer Nystrom [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-1000-1579>)",
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      "package": "Biostrings",
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      "package": "utils",
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    {
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    {
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    "functionalgenomics",
    "generegulation",
    "motifannotation",
    "motifdiscovery",
    "sequencematching",
    "software"
  ],
  "_stars": 54,
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/memes.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/snystrom/memes",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "add_sequence",
    "ame_compare_heatmap_methods",
    "check_meme_install",
    "drop_best_match",
    "force_best_match",
    "get_sequence",
    "has_duplicate_motifs",
    "importAme",
    "importDremeXML",
    "importFimo",
    "importMeme",
    "importStremeXML",
    "importTomTomXML",
    "meme_is_installed",
    "nest_tomtom",
    "plot_ame_heatmap",
    "plot_sequence_heatmap",
    "remove_duplicate_motifs",
    "runAme",
    "runDreme",
    "runFimo",
    "runMeme",
    "runStreme",
    "runTomTom",
    "update_best_match",
    "view_tomtom_hits",
    "write_fasta"
  ],
  "_datasets": [
    {
      "name": "example_ame",
      "title": "Example runAme() output",
      "object": "example_ame",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "example_ame_large",
      "title": "runAme() output for example_chip_summits split by binding description",
      "object": "example_ame_large",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "example_chip_summits",
      "title": "Annotated Transcription Factor ChIP-seq summits",
      "object": "example_chip_summits",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_dreme",
      "title": "Example runDreme() output",
      "object": "example_dreme",
      "class": [
        "universalmotif_df",
        "data.frame"
      ],
      "fields": [
        "motif",
        "name",
        "altname",
        "family",
        "organism",
        "consensus",
        "alphabet",
        "strand",
        "icscore",
        "nsites",
        "bkgsites",
        "pval",
        "qval",
        "eval",
        "type",
        "bkg",
        "rank",
        "seq",
        "length",
        "positive_hits",
        "negative_hits",
        "unerased_evalue",
        "positive_total",
        "negative_total",
        "pos_frac",
        "neg_frac"
      ],
      "rows": 2,
      "table": false,
      "tojson": false
    },
    {
      "name": "example_dreme_by_binding",
      "title": "runDreme() output for example_chip_summits split by binding description",
      "object": "example_dreme_by_binding",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_dreme_tomtom",
      "title": "Example runDreme() output after passing to runTomTom()",
      "object": "example_dreme_tomtom",
      "class": [
        "universalmotif_df",
        "data.frame"
      ],
      "fields": [
        "motif",
        "name",
        "altname",
        "family",
        "organism",
        "consensus",
        "alphabet",
        "strand",
        "icscore",
        "nsites",
        "bkgsites",
        "pval",
        "qval",
        "eval",
        "type",
        "bkg",
        "rank",
        "seq",
        "length",
        "positive_hits",
        "negative_hits",
        "unerased_evalue",
        "positive_total",
        "negative_total",
        "pos_frac",
        "neg_frac",
        "best_match_name",
        "best_match_altname",
        "best_db_name",
        "best_match_offset",
        "best_match_pval",
        "best_match_eval",
        "best_match_qval",
        "best_match_strand",
        "best_match_motif",
        "tomtom"
      ],
      "rows": 2,
      "table": false,
      "tojson": false
    },
    {
      "name": "example_fimo",
      "title": "Example runFimo() output",
      "object": "example_fimo",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_peaks",
      "title": "Example ChIP-seq peaks",
      "object": "example_peaks",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_rnaseq",
      "title": "RNAseq data from Early and Late Drosophila wings",
      "object": "example_rnaseq",
      "class": [
        "grouped_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "symbol",
        "time",
        "fpkm"
      ],
      "rows": 744,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_tomtom",
      "title": "Example runTomTom() output",
      "object": "example_tomtom",
      "class": [
        "universalmotif_df",
        "data.frame"
      ],
      "fields": [
        "motif",
        "name",
        "altname",
        "family",
        "organism",
        "consensus",
        "alphabet",
        "strand",
        "icscore",
        "nsites",
        "bkgsites",
        "pval",
        "qval",
        "eval",
        "type",
        "bkg",
        "best_match_name",
        "best_match_altname",
        "best_db_name",
        "best_match_offset",
        "best_match_pval",
        "best_match_eval",
        "best_match_qval",
        "best_match_strand",
        "best_match_motif",
        "tomtom"
      ],
      "rows": 1,
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "add_sequence",
      "title": "Add nucleic acid sequence of regions to metadata column",
      "topics": [
        "add_sequence"
      ]
    },
    {
      "page": "ame_compare_heatmap_methods",
      "title": "Compare AME heatmap methods",
      "topics": [
        "ame_compare_heatmap_methods"
      ]
    },
    {
      "page": "check_meme_install",
      "title": "Check user's MEME install",
      "topics": [
        "check_meme_install"
      ]
    },
    {
      "page": "drop_best_match",
      "title": "Drop best match columns from tomtom results",
      "topics": [
        "drop_best_match"
      ]
    },
    {
      "page": "example_ame",
      "title": "Example runAme() output",
      "topics": [
        "example_ame"
      ]
    },
    {
      "page": "example_ame_large",
      "title": "runAme() output for example_chip_summits split by binding description",
      "topics": [
        "example_ame_large"
      ]
    },
    {
      "page": "example_chip_summits",
      "title": "Annotated Transcription Factor ChIP-seq summits",
      "topics": [
        "example_chip_summits"
      ]
    },
    {
      "page": "example_dreme",
      "title": "Example runDreme() output",
      "topics": [
        "example_dreme"
      ]
    },
    {
      "page": "example_dreme_by_binding",
      "title": "runDreme() output for example_chip_summits split by binding description",
      "topics": [
        "example_dreme_by_binding"
      ]
    },
    {
      "page": "example_dreme_tomtom",
      "title": "Example runDreme() output after passing to runTomTom()",
      "topics": [
        "example_dreme_tomtom"
      ]
    },
    {
      "page": "example_fimo",
      "title": "Example runFimo() output",
      "topics": [
        "example_fimo"
      ]
    },
    {
      "page": "example_peaks",
      "title": "Example ChIP-seq peaks",
      "topics": [
        "example_peaks"
      ]
    },
    {
      "page": "example_rnaseq",
      "title": "RNAseq data from Early and Late Drosophila wings",
      "topics": [
        "example_rnaseq"
      ]
    },
    {
      "page": "example_tomtom",
      "title": "Example runTomTom() output",
      "topics": [
        "example_tomtom"
      ]
    },
    {
      "page": "force_best_match",
      "title": "Force best tomtom match by id",
      "topics": [
        "force_best_match"
      ]
    },
    {
      "page": "get_sequence",
      "title": "Get sequence from GRanges",
      "topics": [
        "get_sequence"
      ]
    },
    {
      "page": "has_duplicate_motifs",
      "title": "Check for duplicated motif matrices",
      "topics": [
        "has_duplicate_motifs"
      ]
    },
    {
      "page": "importAme",
      "title": "Parse AME output",
      "concept": [
        "import"
      ],
      "topics": [
        "importAme"
      ]
    },
    {
      "page": "importDremeXML",
      "title": "Import Dreme output from previous run",
      "topics": [
        "importDremeXML"
      ]
    },
    {
      "page": "importFimo",
      "title": "Import FIMO results",
      "topics": [
        "importFimo"
      ]
    },
    {
      "page": "importMeme",
      "title": "Import MEME results",
      "topics": [
        "importMeme"
      ]
    },
    {
      "page": "importStremeXML",
      "title": "Import Streme output from previous run",
      "topics": [
        "importStremeXML"
      ]
    },
    {
      "page": "importTomTomXML",
      "title": "Import tomtom data from previous run",
      "topics": [
        "importTomTomXML"
      ]
    },
    {
      "page": "meme_is_installed",
      "title": "Returns logical vector indicating valid MEME-Suite install status",
      "topics": [
        "meme_is_installed"
      ]
    },
    {
      "page": "nest_tomtom",
      "title": "Nest TomTom results columns into a data.frame column named \"tomtom\"",
      "topics": [
        "nest_tomtom"
      ]
    },
    {
      "page": "plot_ame_heatmap",
      "title": "Plot AME heatmap clustered by similarity in detected motifs",
      "topics": [
        "plot_ame_heatmap"
      ]
    },
    {
      "page": "plot_sequence_heatmap",
      "title": "Visualize a heatmap of aligned sequences",
      "topics": [
        "plot_sequence_heatmap"
      ]
    },
    {
      "page": "remove_duplicate_motifs",
      "title": "Remove duplicated motif entries",
      "topics": [
        "remove_duplicate_motifs"
      ]
    },
    {
      "page": "runAme",
      "title": "Motif enrichment using AME",
      "topics": [
        "runAme",
        "runAme.BStringSetList",
        "runAme.default",
        "runAme.list"
      ]
    },
    {
      "page": "runDreme",
      "title": "Denovo motif discovery of target regions using DREME",
      "topics": [
        "runDreme"
      ]
    },
    {
      "page": "runFimo",
      "title": "Find instances of motifs using FIMO",
      "topics": [
        "runFimo"
      ]
    },
    {
      "page": "runMeme",
      "title": "Identify motifs with MEME",
      "topics": [
        "runMeme",
        "runMeme.BStringSetList",
        "runMeme.default",
        "runMeme.list"
      ]
    },
    {
      "page": "runStreme",
      "title": "Denovo motif discovery of target regions using STREME",
      "topics": [
        "runStreme"
      ]
    },
    {
      "page": "runTomTom",
      "title": "Run TomTom on target motifs",
      "topics": [
        "runTomTom"
      ]
    },
    {
      "page": "update_best_match",
      "title": "Update best match info by ranking of tomtom data",
      "topics": [
        "update_best_match"
      ]
    },
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