{
  "_id": "6a1d29871d7bb097a0a386b8",
  "Package": "moanin",
  "Title": "An R Package for Time Course RNASeq Data Analysis",
  "Version": "1.21.0",
  "Authors@R": "c(person(\"Elizabeth\", \"Purdom\", email=\"epurdom@stat.berkeley.edu\",\nrole=c(\"aut\"),\ncomment=c(\"orcid\"=\"https://orcid.org/0000-0001-9455-7990\")),\nperson(\"Nelle\", \"Varoquaux\", role=c(\"aut\", \"cre\"),\nemail=\"nelle.varoquaux@gmail.com\",\ncomment=c(orcid=\"https://orcid.org/0000-0002-8748-6546\")))",
  "Description": "Simple and efficient workflow for time-course gene\nexpression data, built on publictly available open-source\nprojects hosted on CRAN and bioconductor. moanin provides\nhelper functions for all the steps required for analysing\ntime-course data using functional data analysis: (1) functional\nmodeling of the timecourse data; (2) differential expression\nanalysis; (3) clustering; (4) downstream analysis.",
  "VignetteBuilder": "knitr",
  "License": "BSD 3-clause License + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "false",
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  "biocViews": "TimeCourse, GeneExpression, RNASeq, Microarray,\nDifferentialExpression, Clustering",
  "Config/pak/sysreqs": "libgmp3-dev libicu-dev libpng-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:28 UTC",
  "RemoteUrl": "https://github.com/bioc/moanin",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:39:36 UTC",
    "User": "root"
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  "Author": "Elizabeth Purdom [aut] (ORCID: <https://orcid.org/0000-0001-9455-7990>),\nNelle Varoquaux [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8748-6546>)",
  "Maintainer": "Nelle Varoquaux <nelle.varoquaux@gmail.com>",
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  "_published": "2026-06-01T06:41:11.276Z",
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    "geneexpression",
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    "microarray",
    "differentialexpression",
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    "consensus_matrix",
    "create_go_term_mapping",
    "create_moanin_model",
    "create_timepoints_contrasts",
    "DE_timecourse",
    "DE_timepoints",
    "degrees_of_freedom",
    "discont_basis",
    "estimate_log_fold_change",
    "find_enriched_go_terms",
    "get_auc_similarity_scores",
    "get_log_data",
    "group_variable",
    "group_variable_name",
    "group_variable_name<-",
    "group_variable<-",
    "log_transform",
    "perWeek_barplot",
    "plot_cdf_consensus",
    "plot_model_explorer",
    "plot_splines_data",
    "pvalues_fisher_method",
    "rescale_values",
    "show",
    "spline_formula",
    "splines_kmeans",
    "splines_kmeans_predict",
    "splines_kmeans_score_and_label",
    "time_by_group_variable",
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    "time_variable_name",
    "time_variable_name<-",
    "time_variable<-"
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      "rows": 500,
      "table": true,
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    },
    {
      "name": "testGenesGO",
      "title": "Small data set for running examples",
      "object": "exampleData",
      "file": "exampleData.rda",
      "class": [
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      ],
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        "refseq_mrna"
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      "table": true,
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    },
    {
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      "title": "Small data set for running examples",
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        "Replicate",
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  "_help": [
    {
      "page": "consensus_matrix",
      "title": "Compute consensus matrix from labels",
      "topics": [
        "consensus_matrix"
      ]
    },
    {
      "page": "DE_timecourse",
      "title": "Run spline models and test for DE of contrasts.",
      "topics": [
        "DE_timecourse",
        "DE_timecourse,Moanin-method"
      ]
    },
    {
      "page": "DE_timepoints",
      "title": "Fit weekly differential expression analysis",
      "topics": [
        "create_timepoints_contrasts",
        "create_timepoints_contrasts,Moanin-method",
        "DE_timepoints",
        "DE_timepoints,Moanin-method"
      ]
    },
    {
      "page": "discont_basis",
      "title": "Provides set of basis functions on either side of a time point, allowing for a discontinuity in the fitted functions",
      "topics": [
        "discont_basis"
      ]
    },
    {
      "page": "estimate_log_fold_change",
      "title": "Estimates log fold change",
      "topics": [
        "estimate_log_fold_change",
        "estimate_log_fold_change,Moanin-method"
      ]
    },
    {
      "page": "exampleData",
      "title": "Small data set for running examples",
      "topics": [
        "exampleData",
        "testData",
        "testGenesGO",
        "testMeta"
      ]
    },
    {
      "page": "find_enriched_go_terms",
      "title": "Find enriched GO terms",
      "topics": [
        "create_go_term_mapping",
        "find_enriched_go_terms"
      ]
    },
    {
      "page": "Moanin-class",
      "title": "Class Moanin",
      "topics": [
        "create_moanin_model",
        "create_moanin_model,data.frame-method",
        "create_moanin_model,DataFrame-method",
        "create_moanin_model,matrix-method",
        "create_moanin_model,SummarizedExperiment-method",
        "Moanin",
        "Moanin-class"
      ]
    },
    {
      "page": "Moanin-methods",
      "title": "Helper methods for the Moanin class",
      "topics": [
        "basis_matrix",
        "basis_matrix,Moanin-method",
        "degrees_of_freedom",
        "degrees_of_freedom,Moanin-method",
        "get_log_data",
        "get_log_data,Moanin-method",
        "group_variable",
        "group_variable,Moanin-method",
        "group_variable<-",
        "group_variable<-,Moanin-method",
        "group_variable_name",
        "group_variable_name,Moanin-method",
        "group_variable_name<-",
        "group_variable_name<-,Moanin-method",
        "log_transform",
        "log_transform,Moanin-method",
        "Moanin-methods",
        "show",
        "show,Moanin-method",
        "spline_formula",
        "spline_formula,Moanin-method",
        "time_by_group_variable",
        "time_by_group_variable,Moanin-method",
        "time_variable",
        "time_variable,Moanin-method",
        "time_variable<-",
        "time_variable<-,Moanin-method",
        "time_variable_name",
        "time_variable_name,Moanin-method",
        "time_variable_name<-",
        "time_variable_name<-,Moanin-method",
        "[,Moanin,ANY,ANY,ANY-method",
        "[,Moanin,ANY,character,ANY-method",
        "[,Moanin,ANY,logical,ANY-method",
        "[,Moanin,ANY,numeric,ANY-method"
      ]
    },
    {
      "page": "perWeek_barplot",
      "title": "Creates barplot of results of per-timepoint comparison",
      "topics": [
        "perWeek_barplot"
      ]
    },
    {
      "page": "get_auc_similarity_scores",
      "title": "Evaluate the consensus between sets of clusterings",
      "topics": [
        "get_auc_similarity_scores",
        "plot_cdf_consensus",
        "plot_model_explorer"
      ]
    },
    {
      "page": "plot_splines_data",
      "title": "Plotting splines",
      "topics": [
        "plot_splines_data",
        "plot_splines_data,Moanin,data.frame-method",
        "plot_splines_data,Moanin,DataFrame-method",
        "plot_splines_data,Moanin,matrix-method",
        "plot_splines_data,Moanin,missing-method",
        "plot_splines_data,Moanin,numeric-method"
      ]
    },
    {
      "page": "pvalues_fisher_method",
      "title": "Fisher's method to combine pvalues",
      "topics": [
        "pvalues_fisher_method"
      ]
    },
    {
      "page": "rescale_values",
      "title": "Rescales rows of data to be between 0 and 1",
      "topics": [
        "NULL-method",
        "rescale_values",
        "rescale_values,",
        "rescale_values,missing-method",
        "rescale_values,Moanin-method",
        "rescale_values,NULL-method"
      ]
    },
    {
      "page": "splines_kmeans",
      "title": "Performs splines clustering using K-means",
      "topics": [
        "splines_kmeans",
        "splines_kmeans,Moanin-method"
      ]
    },
    {
      "page": "splines_kmeans_score_and_label",
      "title": "Assign score and labels from raw data",
      "topics": [
        "splines_kmeans_predict",
        "splines_kmeans_predict,Moanin-method",
        "splines_kmeans_score_and_label",
        "splines_kmeans_score_and_label,Moanin-method"
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    }
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    "XVector",
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  "_vignettes": [
    {
      "source": "documentation.Rmd",
      "filename": "documentation.html",
      "title": "moanin: An R Package for Time Course RNASeq Data Analysis",
      "engine": "knitr::knitr",
      "headings": [
        "Setup",
        "Set up moanin class",
        "Moanin and SummarizedExperiment",
        "Log-tranformation",
        "Weekly differential expression analysis",
        "Compare change across two time points",
        "Time-course differential expression analysis between two groups",
        "Visualizing Genes of Interest",
        "Clustering of time-course data",
        "Assigning genes to clusters"
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      "created": "2020-06-22 08:24:25",
      "modified": "2021-07-28 07:11:22",
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