{
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  "Package": "sagenhaft",
  "Version": "1.83.0",
  "Date": "2020-01-10",
  "Title": "Collection of functions for reading and comparing SAGE libraries",
  "Author": "Tim Beissbarth <tim.beissbarth@bioinf.med.uni-goettingen.de>,\nwith contributions from Gordon Smyth <smyth@wehi.edu.au>",
  "Reference": "Beissbarth T, Hyde L, Smyth GK, Job C, Boon WM, Tan SS,\nScott HS, Speed TP: Statistical modeling of sequencing errors\nin SAGE libraries, Bioinformatics, 2004 20(Suppl. 1):i31-9.",
  "Maintainer": "Tim Beissbarth\n<tim.beissbarth@bioinf.med.uni-goettingen.de>",
  "Description": "This package implements several functions useful for\nanalysis of gene expression data by sequencing tags as done in\nSAGE (Serial Analysis of Gene Expressen) data, i.e. extraction\nof a SAGE library from sequence files, sequence error\ncorrection, library comparison. Sequencing error correction is\nimplementing using an Expectation Maximization Algorithm based\non a Mixture Model of tag counts.",
  "biocViews": "SAGE",
  "License": "GPL (>= 2)",
  "URL": "http://www.bioinf.med.uni-goettingen.de",
  "git_url": "https://git.bioconductor.org/packages/sagenhaft",
  "git_branch": "RELEASE_3_10",
  "git_last_commit": "c49299a",
  "git_last_commit_date": "2019-10-29",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 22:35:13 UTC",
    "User": "root"
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:52 UTC",
  "RemoteUrl": "https://github.com/bioc/sagenhaft",
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  "_created": "2026-07-04T22:35:13.000Z",
  "_published": "2026-07-04T22:38:31.376Z",
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    "warning": 5,
    "note": 15
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  "_selfowned": true,
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  "_updates": [
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    },
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      "version": "1.82.0",
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  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "manual.pdf"
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  "_realowner": "bioc",
  "_cranurl": false,
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    "compare.lib.pair",
    "compute.sequence.neighbors",
    "compute.unique.tags",
    "create.matrix.csr",
    "difference.scatter.plot",
    "em.estimate.error.given",
    "estimate.errors.mean",
    "extract.ditags",
    "extract.lib.from.directory",
    "extract.lib.from.zip",
    "extract.library.tags",
    "plot.sage.library",
    "plot.sage.library.comparison",
    "print.sage.library",
    "print.sage.library.comparison",
    "read.phd.file",
    "read.sage.library",
    "read.sage.library.comparison",
    "read.seq.qual.filepair",
    "reestimate.lib.from.tagcounts",
    "remove.sage.artifacts",
    "revcomp",
    "sage.test",
    "sagelibrary.simulate",
    "summary.sage.library",
    "summary.sage.library.comparison",
    "table.sparse",
    "tagmatrix2tagnum",
    "tagnum2tagmatrix",
    "tagnum2tagsequence",
    "tagsequence2tagnum",
    "write.sage.library",
    "write.sage.library.comparison"
  ],
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    {
      "name": "SAGEartifacts",
      "title": "Functions for SAGE library extraction",
      "object": "SAGEartifacts",
      "file": "SAGEartifacts.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "tag",
        "type"
      ],
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      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "error.correction",
      "title": "Estimate sequencing errors and compute corrected counts",
      "topics": [
        "compute.sequence.neighbors",
        "em.estimate.error.given",
        "estimate.errors.mean"
      ]
    },
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      "page": "extract.lib",
      "title": "Functions for SAGE library extraction",
      "topics": [
        "combine.libs",
        "compute.unique.tags",
        "extract.ditags",
        "extract.lib.from.directory",
        "extract.lib.from.zip",
        "extract.library.tags",
        "read.phd.file",
        "read.seq.qual.filepair",
        "reestimate.lib.from.tagcounts",
        "remove.sage.artifacts",
        "SAGEartifacts"
      ]
    },
    {
      "page": "sage.library",
      "title": "Class sage.library",
      "concept": [
        "SAGE"
      ],
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        "plot.sage.library",
        "print.sage.library",
        "read.sage.library",
        "summary.sage.library",
        "write.sage.library"
      ]
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      "title": "Class sage.library.comparison",
      "concept": [
        "SAGE"
      ],
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        "plot.sage.library.comparison",
        "print.sage.library.comparison",
        "read.sage.library.comparison",
        "summary.sage.library.comparison",
        "write.sage.library.comparison"
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    },
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      "page": "sage.test",
      "title": "Compare Two SAGE Libraries",
      "topics": [
        "sage.test"
      ]
    },
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      "title": "Utilities",
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        "difference.scatter.plot",
        "revcomp",
        "table.sparse",
        "tagmatrix2tagnum",
        "tagnum2tagmatrix",
        "tagnum2tagsequence",
        "tagsequence2tagnum"
      ]
    },
    {
      "page": "sagelibrary.simulate",
      "title": "Simulate SAGE libraries",
      "topics": [
        "sagelibrary.simulate"
      ]
    }
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      "headings": [
        "Overview",
        "SAGE",
        "Base-calling and extraction of SAGE tags",
        "Sequence Error correction",
        "Comparison of SAGE libraries",
        "Example"
      ],
      "created": "2013-11-01 19:53:19",
      "modified": "2013-11-01 19:53:19",
      "commits": 1
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