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  "Package": "transite",
  "Title": "RNA-binding protein motif analysis",
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  "Description": "transite is a computational method that allows\ncomprehensive analysis of the regulatory role of RNA-binding\nproteins in various cellular processes by leveraging\npreexisting gene expression data and current knowledge of\nbinding preferences of RNA-binding proteins.",
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    "differentialexpression",
    "microarray",
    "mrnamicroarray",
    "genetics",
    "genesetenrichment",
    "cpp"
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    "calculate_kmer_enrichment",
    "calculate_local_consistency",
    "calculate_motif_enrichment",
    "calculate_transcript_mc",
    "check_kmers",
    "classify_spectrum",
    "compute_kmer_enrichment",
    "create_kmer_motif",
    "create_kmer_origin_list",
    "create_matrix_motif",
    "draw_volcano_plot",
    "estimate_significance",
    "estimate_significance_core",
    "generate_iupac_by_kmers",
    "generate_iupac_by_matrix",
    "generate_kmers",
    "generate_kmers_from_iupac",
    "generate_permuted_enrichments",
    "geometric_mean",
    "get_adj_r_squared",
    "get_consistency_score",
    "get_consistency_score_n",
    "get_consistency_score_p_value",
    "get_heptamers",
    "get_hexamers",
    "get_id",
    "get_iupac",
    "get_model_degree",
    "get_model_f_statistic",
    "get_model_f_statistic_p_value",
    "get_model_residuals",
    "get_model_slope",
    "get_motif_by_id",
    "get_motif_by_rbp",
    "get_motif_matrix",
    "get_motifs",
    "get_motifs_meta_info",
    "get_ppm",
    "get_rbps",
    "get_source",
    "get_species",
    "get_type",
    "get_width",
    "init_iupac_lookup_table",
    "p_combine",
    "plot",
    "run_kmer_spma",
    "run_kmer_tsma",
    "run_matrix_spma",
    "run_matrix_tsma",
    "score_sequences",
    "score_spectrum",
    "score_transcripts",
    "set_motifs",
    "subdivide_data"
  ],
  "_datasets": [
    {
      "name": "ge",
      "title": "Toy Gene Expression Data Set",
      "object": "ge",
      "file": "ge.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "kmers_enrichment",
      "title": "Example _k_-mer Enrichment Data",
      "object": "kmers_enrichment",
      "file": "kmers_enrichment.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "kmer",
        "foreground_count",
        "background_count",
        "enrichment",
        "p_value",
        "adj_p_value"
      ],
      "rows": 4096,
      "table": true,
      "tojson": true
    },
    {
      "name": "motifs",
      "title": "Transite Motif Database",
      "object": "motifs",
      "file": "motifs.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "toy_motif_matrix",
      "title": "Toy Motif Matrix",
      "object": "toy_motif_matrix",
      "file": "toy_motif_matrix.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "A",
        "C",
        "G",
        "U"
      ],
      "rows": 7,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculate_kmer_enrichment",
      "title": "_k_-mer Enrichment between Foreground and Background Sets",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "calculate_kmer_enrichment"
      ]
    },
    {
      "page": "calculate_local_consistency",
      "title": "Local Consistency Score",
      "topics": [
        "calculate_local_consistency"
      ]
    },
    {
      "page": "calculate_motif_enrichment",
      "title": "Binding Site Enrichment Value Calculation",
      "concept": [
        "matrix functions"
      ],
      "topics": [
        "calculate_motif_enrichment"
      ]
    },
    {
      "page": "calculate_transcript_mc",
      "title": "Motif Enrichment calculation",
      "topics": [
        "calculate_transcript_mc"
      ]
    },
    {
      "page": "check_kmers",
      "title": "Check Validity of Set of _k_-mers",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "check_kmers"
      ]
    },
    {
      "page": "classify_spectrum",
      "title": "Simple spectrum classifier based on empirical thresholds",
      "concept": [
        "SPMA functions"
      ],
      "topics": [
        "classify_spectrum"
      ]
    },
    {
      "page": "compute_kmer_enrichment",
      "title": "_k_-mer Enrichment between Foreground and Background Sets",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "compute_kmer_enrichment"
      ]
    },
    {
      "page": "count_homopolymer_corrected_kmers",
      "title": "Correction for Homopolymeric Stretches",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "count_homopolymer_corrected_kmers"
      ]
    },
    {
      "page": "create_kmer_motif",
      "title": "Creates Transite motif object from character vector of _k_-mers",
      "topics": [
        "create_kmer_motif"
      ]
    },
    {
      "page": "create_kmer_origin_list",
      "title": "Create _k_-mer lists with their original sequences",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "create_kmer_origin_list"
      ]
    },
    {
      "page": "create_matrix_motif",
      "title": "Creates Transite motif object from position weight matrix",
      "topics": [
        "create_matrix_motif"
      ]
    },
    {
      "page": "draw_volcano_plot",
      "title": "_k_-mer Enrichment Volcano Plot",
      "concept": [
        "TSMA functions",
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "draw_volcano_plot"
      ]
    },
    {
      "page": "estimate_significance",
      "title": "Permutation Test Based Significance of Observed Mean",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "estimate_significance"
      ]
    },
    {
      "page": "estimate_significance_core",
      "title": "Significance of Observed Mean",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "estimate_significance_core"
      ]
    },
    {
      "page": "ge",
      "title": "Toy Gene Expression Data Set",
      "topics": [
        "ge"
      ]
    },
    {
      "page": "generate_iupac_by_kmers",
      "title": "Generates IUPAC code for a character vector of _k_-mers",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "generate_iupac_by_kmers"
      ]
    },
    {
      "page": "generate_iupac_by_matrix",
      "title": "Generates IUPAC code for motif matrix",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "generate_iupac_by_matrix"
      ]
    },
    {
      "page": "generate_kmers",
      "title": "_k_-mer Counts for Sequence Set",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "generate_kmers"
      ]
    },
    {
      "page": "generate_kmers_from_iupac",
      "title": "Generates all _k_-mers for IUPAC string",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "generate_kmers_from_iupac"
      ]
    },
    {
      "page": "generate_permuted_enrichments",
      "title": "Generate Random Permutations of the Enrichment Data",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "generate_permuted_enrichments"
      ]
    },
    {
      "page": "geometric_mean",
      "title": "Geometric Mean",
      "topics": [
        "geometric_mean"
      ]
    },
    {
      "page": "get_motif_by_id",
      "title": "Retrieve motif objects by id",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motif_by_id"
      ]
    },
    {
      "page": "get_motif_by_rbp",
      "title": "Retrieve motif objects by gene symbol",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motif_by_rbp"
      ]
    },
    {
      "page": "get_motifs",
      "title": "Retrieve list of all motifs",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motifs"
      ]
    },
    {
      "page": "get_motifs_meta_info",
      "title": "Displays motif meta information.",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motifs_meta_info"
      ]
    },
    {
      "page": "get_ppm",
      "title": "Get Position Probability Matrix (PPM) from motif object",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_ppm"
      ]
    },
    {
      "page": "init_iupac_lookup_table",
      "title": "Initializes the IUPAC lookup table",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "init_iupac_lookup_table"
      ]
    },
    {
      "page": "kmers_enrichment",
      "title": "Example _k_-mer Enrichment Data",
      "topics": [
        "kmers_enrichment"
      ]
    },
    {
      "page": "motifs",
      "title": "Transite Motif Database",
      "topics": [
        "motifs"
      ]
    },
    {
      "page": "p_combine",
      "title": "P-value aggregation",
      "topics": [
        "p_combine"
      ]
    },
    {
      "page": "RBPMotif-class",
      "title": "An S4 class to represent a RBPMotif",
      "topics": [
        ".RBPMotif",
        "get_heptamers",
        "get_heptamers,RBPMotif-method",
        "get_hexamers",
        "get_hexamers,RBPMotif-method",
        "get_id",
        "get_id,RBPMotif-method",
        "get_iupac",
        "get_iupac,RBPMotif-method",
        "get_motif_matrix",
        "get_motif_matrix,RBPMotif-method",
        "get_rbps",
        "get_rbps,RBPMotif-method",
        "get_source",
        "get_source,RBPMotif-method",
        "get_species",
        "get_species,RBPMotif-method",
        "get_type",
        "get_type,RBPMotif-method",
        "get_width",
        "get_width,RBPMotif-method",
        "RBPMotif-class",
        "show,RBPMotif-method"
      ]
    },
    {
      "page": "run_kmer_spma",
      "title": "_k_-mer-based Spectrum Motif Analysis",
      "concept": [
        "SPMA functions",
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "run_kmer_spma"
      ]
    },
    {
      "page": "run_kmer_tsma",
      "title": "_k_-mer-based Transcript Set Motif Analysis",
      "concept": [
        "TSMA functions",
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "run_kmer_tsma"
      ]
    },
    {
      "page": "run_matrix_spma",
      "title": "Matrix-based Spectrum Motif Analysis",
      "concept": [
        "SPMA functions",
        "matrix functions"
      ],
      "topics": [
        "run_matrix_spma"
      ]
    },
    {
      "page": "run_matrix_tsma",
      "title": "Matrix-based Transcript Set Motif Analysis",
      "concept": [
        "TSMA functions",
        "matrix functions"
      ],
      "topics": [
        "run_matrix_tsma"
      ]
    },
    {
      "page": "score_sequences",
      "title": "Score Sequences with PWM",
      "topics": [
        "score_sequences"
      ]
    },
    {
      "page": "score_spectrum",
      "title": "Calculates spectrum scores and creates spectrum plots",
      "concept": [
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      "title": "Scores transcripts with position weight matrices",
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      "page": "score_transcripts_single_motif",
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      "title": "Set Transite motif database",
      "concept": [
        "motif functions"
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      "topics": [
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    },
    {
      "page": "SpectrumScore-class",
      "title": "An S4 class to represent a scored spectrum",
      "topics": [
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        "get_consistency_score",
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        "get_model_f_statistic",
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      "page": "toy_motif_matrix",
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      "source": "spma.Rmd",
      "filename": "spma.html",
      "title": "Spectrum Motif Analysis (SPMA)",
      "author": "Konstantin Krismer",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Results",
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      "created": "2018-09-18 21:57:58",
      "modified": "2020-08-25 15:05:46",
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