{
  "_id": "6acce98ca14063b82c3aa5ff",
  "Package": "TiDEomics",
  "Title": "Time-course Differential Expression analysis of omics data",
  "Version": "0.99.5",
  "Date": "2026-07-31",
  "Authors@R": "person(\"Tianen\", \"He\",\nemail = \"tianen.he@ndm.ox.ac.uk\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6864-0723\"))",
  "Description": "TiDEomics provides a comprehensive workflow for\nmulti-group time-course omics data analysis, analysing\ntime-dominant, group-dominant, and group-specific temporal\neffects through pairwise differential expression, variance\ndecomposition, and co-expression module analysis (WGCNA). The\npackage integrates quality control, data processing, functional\nenrichment, and extensive visualisation. It supports datasets\nwith missing values (e.g., mass spectrometry-based proteomics),\nand operates on SummarizedExperiment objects to ensure\ncompatibility with the Bioconductor ecosystem.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/hte123/TiDEomics,\nhttps://hte123.github.io/TiDEomics",
  "BugReports": "https://github.com/hte123/TiDEomics/issues",
  "biocViews": "Software, GeneExpression, DifferentialExpression,\nProteomics, Transcriptomics, TimeCourse, MultipleComparison,\nPathways, Visualization, MassSpectrometry, QualityControl",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "LazyData": "false",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl python3 zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-31 18:22:25 UTC",
  "RemoteUrl": "https://github.com/bioc/TiDEomics",
  "RemoteRef": "HEAD",
  "RemoteSha": "ca26312c86214fd3ec8d103e330224611463edd3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-12 13:46:13 UTC",
    "User": "root"
  },
  "Author": "Tianen He [aut, cre] (ORCID: <https://orcid.org/0000-0001-6864-0723>)",
  "Maintainer": "Tianen He <tianen.he@ndm.ox.ac.uk>",
  "_user": "bioc",
  "_type": "src",
  "_file": "TiDEomics_0.99.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/8d1bd3ca5579ae5fcdde6d8dbd6ecb196c7947666d021703bc9b01d972cda9fd",
  "_filesize": 4583696,
  "_sha256": "8d1bd3ca5579ae5fcdde6d8dbd6ecb196c7947666d021703bc9b01d972cda9fd",
  "_expires": "2027-01-20T14:07:05.000Z",
  "_created": "2026-10-12T13:46:13.000Z",
  "_published": "2026-10-12T14:07:07.841Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 4
  },
  "_upstream": "https://github.com/bioc/TiDEomics",
  "_commit": {
    "id": "ca26312c86214fd3ec8d103e330224611463edd3",
    "author": "Tianen He <tianen.he@ndm.ox.ac.uk>",
    "committer": "Tianen He <tianen.he@ndm.ox.ac.uk>",
    "message": "v0.99.5, improve assay validation, fix vignette\n\nUpdate version to 0.99.5. Update `.match_assay()` to require a single assay index / name and disallow NULL. Adjust `plot_trend()` default title behaviour internally. Add tests accordingly. Fix the vignette bug to use `ylab` in `plot_segments()`.\n",
    "time": 1785522145
  },
  "_maintainer": {
    "name": "Tianen He",
    "email": "tianen.he@ndm.ox.ac.uk",
    "login": "hte123",
    "description": "",
    "uuid": 59926992,
    "orcid": "0000-0001-6864-0723"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114841379880,
      "time": 248,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11752100128"
    },
    {
      "job": 114841380080,
      "time": 1135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11751977982"
    },
    {
      "job": 114841380142,
      "time": 1178,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11751454634"
    },
    {
      "job": 114841380106,
      "time": 1157,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11752620646"
    },
    {
      "job": 114841379979,
      "time": 721,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11751427715"
    },
    {
      "job": 114837465215,
      "time": 577,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11751405838"
    },
    {
      "job": 114841379892,
      "time": 251,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11750949425"
    },
    {
      "job": 114841380065,
      "time": 918,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11752047233"
    },
    {
      "job": 114841380045,
      "time": 1145,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11752480088"
    },
    {
      "job": 114841380000,
      "time": 969,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11752367014"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "clusterProfiler",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "enrichplot",
      "role": "Imports"
    },
    {
      "package": "ggforce",
      "role": "Imports"
    },
    {
      "package": "ggh4x",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggplotify",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggridges",
      "role": "Imports"
    },
    {
      "package": "ggsci",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "PCAtools",
      "role": "Imports"
    },
    {
      "package": "randtests",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "Trendy",
      "role": "Imports"
    },
    {
      "package": "umap",
      "role": "Imports"
    },
    {
      "package": "WGCNA",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.1.0",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "enrichR",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "msigdbr",
      "role": "Suggests"
    },
    {
      "package": "DeeDeeExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-18",
      "n": 9
    },
    {
      "week": "2026-19",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 1
    },
    {
      "week": "2026-22",
      "n": 6
    },
    {
      "week": "2026-23",
      "n": 3
    },
    {
      "week": "2026-24",
      "n": 1
    },
    {
      "week": "2026-26",
      "n": 5
    },
    {
      "week": "2026-27",
      "n": 6
    },
    {
      "week": "2026-30",
      "n": 2
    },
    {
      "week": "2026-31",
      "n": 4
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.5",
      "bioc": "3.24",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "geneexpression",
    "differentialexpression",
    "proteomics",
    "transcriptomics",
    "timecourse",
    "multiplecomparison",
    "pathways",
    "visualization",
    "massspectrometry",
    "qualitycontrol"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "hte123",
      "count": 39,
      "uuid": 59926992
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1179,
    "source": "https://www.bioconductor.org/packages/stats/bioc/TiDEomics"
  },
  "_devurl": "https://github.com/hte123/tideomics",
  "_pkgdown": "https://hte123.github.io/TiDEomics",
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TiDEomics.html"
  ],
  "_homeurl": "https://github.com/hte123/tideomics",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calc_feature_property",
    "calc_mean_sd",
    "create_input",
    "DE_between_group",
    "DE_between_time",
    "decomp_variance",
    "enrich_msigdb",
    "enrichGO_list",
    "enrichGO_rank",
    "enrichR_list",
    "extract_hubs",
    "extract_segment_trends",
    "flatten_DE",
    "flatten_enrich",
    "get_custom_palette",
    "group_specific_features",
    "impute_groups",
    "merge_groups",
    "merge_replicates",
    "normalise_to_start",
    "plot_breakpoints",
    "plot_cor_matrix",
    "plot_cv",
    "plot_DE_between_group",
    "plot_DE_between_time",
    "plot_distribution",
    "plot_GO",
    "plot_ID",
    "plot_missing",
    "plot_modules_h",
    "plot_modules_v",
    "plot_pca",
    "plot_pca_3D",
    "plot_pca_arrows",
    "plot_pca_by_group",
    "plot_segments",
    "plot_trend",
    "plot_umap",
    "plot_umap_by_group",
    "plot_variance",
    "plot_volcano",
    "plot_WGCNA",
    "prepare_tide",
    "prepare_WGCNA",
    "run_Trendy",
    "run_WGCNA",
    "set_custom_palette",
    "split_groups",
    "summarise_feature_property",
    "summarise_module_metrics",
    "summarise_module_pattern",
    "summarise_Trendy",
    "theme_custom",
    "WGCNA_module"
  ],
  "_datasets": [
    {
      "name": "example_go",
      "title": "'enrichGO_list()' output object for runnable examples",
      "object": "example_go",
      "file": "example_go.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_net",
      "title": "'run_WGCNA()' output object for runnable examples",
      "object": "example_net",
      "file": "example_net.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_obj",
      "title": "SummarizedExperiment object for runnable examples",
      "object": "example_obj",
      "file": "example_obj.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_res_list",
      "title": "'run_Trendy' output object for runnable examples",
      "object": "example_res_list",
      "file": "example_res_list.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "tutorial_data",
      "title": "Dataset for TiDEomics tutorial, expression matrix",
      "object": "tutorial_data",
      "file": "tutorial_data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Feature",
        "RNA_untreated_0h_R1_1",
        "RNA_untreated_24h_R1_2",
        "RNA_IFNbeta_2h_R1_1",
        "RNA_IFNbeta_24h_R1_2",
        "RNA_IFNbeta_4h_R1_1",
        "RNA_IFNbeta_6h_R1_1",
        "RNA_IFNbeta_8h_R1_2",
        "RNA_IFNgamma_2h_R1_1",
        "RNA_IFNgamma_24h_R1_2",
        "RNA_IFNgamma_4h_R1_1",
        "RNA_IFNgamma_6h_R1_1",
        "RNA_IFNgamma_8h_R1_2",
        "RNA_LPS_2h_R1_1",
        "RNA_LPS_4h_R1_1",
        "RNA_LPS_6h_R1_1",
        "RNA_LPS_8h_R1_2",
        "RNA_untreated_0h_R2_1",
        "RNA_untreated_24h_R2_2",
        "RNA_untreated_8h_R2_2",
        "RNA_IFNbeta_2h_R2_1",
        "RNA_IFNbeta_24h_R2_2",
        "RNA_IFNbeta_4h_R2_1",
        "RNA_IFNbeta_6h_R2_1",
        "RNA_IFNbeta_8h_R2_2",
        "RNA_IFNgamma_2h_R2_1",
        "RNA_IFNgamma_24h_R2_2",
        "RNA_IFNgamma_4h_R2_1",
        "RNA_IFNgamma_6h_R2_1",
        "RNA_IFNgamma_8h_R2_2",
        "RNA_LPS_2h_R2_1",
        "RNA_LPS_24h_R2_2",
        "RNA_LPS_4h_R2_1",
        "RNA_LPS_6h_R2_1",
        "RNA_LPS_8h_R2_2",
        "RNA_IFNbeta_0h_R1_1",
        "RNA_IFNbeta_0h_R2_1",
        "RNA_IFNgamma_0h_R1_1",
        "RNA_IFNgamma_0h_R2_1",
        "RNA_LPS_0h_R1_1",
        "RNA_LPS_0h_R2_1"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "tutorial_sample_info",
      "title": "Dataset for TiDEomics tutorial, sample information",
      "object": "tutorial_sample_info",
      "file": "tutorial_sample_info.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Group",
        "Time",
        "Replicate",
        "Batch"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calc_feature_property",
      "title": "Calculate feature property",
      "topics": [
        "calc_feature_property"
      ]
    },
    {
      "page": "calc_mean_sd",
      "title": "Calculate mean and SD",
      "topics": [
        "calc_mean_sd"
      ]
    },
    {
      "page": "create_input",
      "title": "Create object",
      "topics": [
        "create_input"
      ]
    },
    {
      "page": "DE_between_group",
      "title": "DE between groups",
      "topics": [
        "DE_between_group"
      ]
    },
    {
      "page": "DE_between_time",
      "title": "DE between time points",
      "topics": [
        "DE_between_time"
      ]
    },
    {
      "page": "decomp_variance",
      "title": "Variance decomposition",
      "topics": [
        "decomp_variance"
      ]
    },
    {
      "page": "enrich_msigdb",
      "title": "Gene set enrichment via MSigDB",
      "topics": [
        "enrich_msigdb"
      ]
    },
    {
      "page": "enrichGO_list",
      "title": "GO enrichment with gene sets",
      "topics": [
        "enrichGO_list"
      ]
    },
    {
      "page": "enrichGO_rank",
      "title": "GO enrichment with ranked gene list",
      "topics": [
        "enrichGO_rank"
      ]
    },
    {
      "page": "enrichR_list",
      "title": "Gene-set enrichment via enrichR",
      "topics": [
        "enrichR_list"
      ]
    },
    {
      "page": "example_go",
      "title": "'enrichGO_list()' output object for runnable examples",
      "topics": [
        "example_go"
      ]
    },
    {
      "page": "example_net",
      "title": "'run_WGCNA()' output object for runnable examples",
      "topics": [
        "example_net"
      ]
    },
    {
      "page": "example_obj",
      "title": "SummarizedExperiment object for runnable examples",
      "topics": [
        "example_obj"
      ]
    },
    {
      "page": "example_res_list",
      "title": "'run_Trendy' output object for runnable examples",
      "topics": [
        "example_res_list"
      ]
    },
    {
      "page": "extract_hubs",
      "title": "Extract hub features from WGCNA modules",
      "topics": [
        "extract_hubs"
      ]
    },
    {
      "page": "extract_segment_trends",
      "title": "Extract feature trends",
      "topics": [
        "extract_segment_trends"
      ]
    },
    {
      "page": "flatten_DE",
      "title": "Flatten nested differential expression results",
      "topics": [
        "flatten_DE"
      ]
    },
    {
      "page": "flatten_enrich",
      "title": "Flatten nested enrichment results",
      "topics": [
        "flatten_enrich"
      ]
    },
    {
      "page": "get_custom_palette",
      "title": "Get custom color palette",
      "topics": [
        "get_custom_palette"
      ]
    },
    {
      "page": "group_specific_features",
      "title": "Group specific features",
      "topics": [
        "group_specific_features"
      ]
    },
    {
      "page": "impute_groups",
      "title": "Impute missing values",
      "topics": [
        "impute_groups"
      ]
    },
    {
      "page": "merge_groups",
      "title": "Merge groups into one object",
      "topics": [
        "merge_groups"
      ]
    },
    {
      "page": "merge_replicates",
      "title": "Merge replicates",
      "topics": [
        "merge_replicates"
      ]
    },
    {
      "page": "normalise_to_start",
      "title": "Normalise to starting time point",
      "topics": [
        "normalise_to_start"
      ]
    },
    {
      "page": "plot_breakpoints",
      "title": "Plot breakpoint distribution",
      "topics": [
        "plot_breakpoints"
      ]
    },
    {
      "page": "plot_cor_matrix",
      "title": "Plot correlation matrix",
      "topics": [
        "plot_cor_matrix"
      ]
    },
    {
      "page": "plot_cv",
      "title": "Plot coefficient of variation (CV)",
      "topics": [
        "plot_cv"
      ]
    },
    {
      "page": "plot_DE_between_group",
      "title": "DE number between groups",
      "topics": [
        "plot_DE_between_group"
      ]
    },
    {
      "page": "plot_DE_between_time",
      "title": "DE number between time points",
      "topics": [
        "plot_DE_between_time"
      ]
    },
    {
      "page": "plot_distribution",
      "title": "Abundance distribution plot",
      "topics": [
        "plot_distribution"
      ]
    },
    {
      "page": "plot_GO",
      "title": "Plot GO enrichment",
      "topics": [
        "plot_GO"
      ]
    },
    {
      "page": "plot_ID",
      "title": "Plot number of identified features",
      "topics": [
        "plot_ID"
      ]
    },
    {
      "page": "plot_missing",
      "title": "Plot missing rate",
      "topics": [
        "plot_missing"
      ]
    },
    {
      "page": "plot_modules_h",
      "title": "Plot modules (horizontal layout)",
      "topics": [
        "plot_modules_h"
      ]
    },
    {
      "page": "plot_modules_v",
      "title": "Plot modules (vertical layout)",
      "topics": [
        "plot_modules_v"
      ]
    },
    {
      "page": "plot_pca",
      "title": "Plot PCA",
      "topics": [
        "plot_pca"
      ]
    },
    {
      "page": "plot_pca_3D",
      "title": "Plot PCA in 3D",
      "topics": [
        "plot_pca_3D"
      ]
    },
    {
      "page": "plot_pca_arrows",
      "title": "Plot PCA with arrows",
      "topics": [
        "plot_pca_arrows"
      ]
    },
    {
      "page": "plot_pca_by_group",
      "title": "Plot PCA by group",
      "topics": [
        "plot_pca_by_group"
      ]
    },
    {
      "page": "plot_segments",
      "title": "Plot segmented regression",
      "topics": [
        "plot_segments"
      ]
    },
    {
      "page": "plot_trend",
      "title": "Plot feature abundance over time",
      "topics": [
        "plot_trend"
      ]
    },
    {
      "page": "plot_umap",
      "title": "Plot UMAP",
      "topics": [
        "plot_umap"
      ]
    },
    {
      "page": "plot_umap_by_group",
      "title": "Plot UMAP by group",
      "topics": [
        "plot_umap_by_group"
      ]
    },
    {
      "page": "plot_variance",
      "title": "Plot variance decomposition",
      "topics": [
        "plot_variance"
      ]
    },
    {
      "page": "plot_volcano",
      "title": "Volcano plot of DE results",
      "topics": [
        "plot_volcano"
      ]
    },
    {
      "page": "plot_WGCNA",
      "title": "Plot WGCNA results",
      "topics": [
        "plot_WGCNA"
      ]
    },
    {
      "page": "prepare_tide",
      "title": "Prepare TiDEomics input",
      "topics": [
        "prepare_tide"
      ]
    },
    {
      "page": "prepare_WGCNA",
      "title": "Prepare data and choose power for WGCNA",
      "topics": [
        "prepare_WGCNA"
      ]
    },
    {
      "page": "run_Trendy",
      "title": "Segmented regression analysis",
      "topics": [
        "run_Trendy"
      ]
    },
    {
      "page": "run_WGCNA",
      "title": "Weighted gene co-expression network analysis",
      "topics": [
        "run_WGCNA"
      ]
    },
    {
      "page": "set_custom_palette",
      "title": "Set custom color palette",
      "topics": [
        "set_custom_palette"
      ]
    },
    {
      "page": "split_groups",
      "title": "Split groups",
      "topics": [
        "split_groups"
      ]
    },
    {
      "page": "summarise_feature_property",
      "title": "Summarise feature properties",
      "topics": [
        "summarise_feature_property"
      ]
    },
    {
      "page": "summarise_module_metrics",
      "title": "Summarise WGCNA module metrics",
      "topics": [
        "summarise_module_metrics"
      ]
    },
    {
      "page": "summarise_module_pattern",
      "title": "Summarise module patterns",
      "topics": [
        "summarise_module_pattern"
      ]
    },
    {
      "page": "summarise_Trendy",
      "title": "Summarise Trendy results",
      "topics": [
        "summarise_Trendy"
      ]
    },
    {
      "page": "theme_custom",
      "title": "Custom ggplot2 theme",
      "topics": [
        "theme_custom"
      ]
    },
    {
      "page": "tutorial_data",
      "title": "Dataset for TiDEomics tutorial, expression matrix",
      "topics": [
        "tutorial_data"
      ]
    },
    {
      "page": "tutorial_sample_info",
      "title": "Dataset for TiDEomics tutorial, sample information",
      "topics": [
        "tutorial_sample_info"
      ]
    },
    {
      "page": "WGCNA_module",
      "title": "Convert WGCNA output to feature-module data frame",
      "topics": [
        "WGCNA_module"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/TiDEomics/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/TiDEomics/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "aisdk",
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "assorthead",
    "backports",
    "base64enc",
    "beachmat",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "callr",
    "car",
    "carData",
    "caTools",
    "checkmate",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "clusterProfiler",
    "codetools",
    "colorspace",
    "commonmark",
    "ComplexHeatmap",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "DOSE",
    "dplyr",
    "dqrng",
    "DT",
    "dynamicTreeCut",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastcluster",
    "fastmap",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "forecast",
    "foreign",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "gdtools",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggforce",
    "ggfun",
    "ggh4x",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggpubr",
    "ggrepel",
    "ggridges",
    "ggsci",
    "ggsignif",
    "ggtangle",
    "ggtree",
    "GlobalOptions",
    "glue",
    "GO.db",
    "GOSemSim",
    "gplots",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "gtools",
    "here",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "impute",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "patchwork",
    "pbapply",
    "pbkrtest",
    "PCAtools",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "polynom",
    "preprocessCore",
    "processx",
    "promises",
    "ps",
    "purrr",
    "quantreg",
    "qvalue",
    "R6",
    "randtests",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppTOML",
    "Rdpack",
    "reformulas",
    "reshape2",
    "reticulate",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "rprojroot",
    "RSpectra",
    "RSQLite",
    "rstatix",
    "rstudioapi",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "ScaledMatrix",
    "scales",
    "scatterpie",
    "segmented",
    "Seqinfo",
    "shape",
    "shiny",
    "shinyFiles",
    "sitmo",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "tibble",
    "tidydr",
    "tidyr",
    "tidyselect",
    "tidytree",
    "timeDate",
    "tinytex",
    "treeio",
    "Trendy",
    "tweenr",
    "umap",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "WGCNA",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "TiDEomics.Rmd",
      "filename": "TiDEomics.html",
      "title": "TiDEomics Tutorial",
      "author": "Tianen He",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Example input",
        "Preprocessing for different data types",
        "Workflow",
        "Data preparation",
        "Optional: custom color palette",
        "Quality control",
        "Normalisation to starting time point",
        "Splitting groups and merging replicates",
        "Sample relationships (correlation, PCA, UMAP)",
        "Pairwise differential expression",
        "Feature properties and classification",
        "Segmented regression analysis",
        "Variance decomposition",
        "WGCNA (co-expression modules)",
        "Functional enrichment",
        "Integrated visualisation of WGCNA modules and functional enrichment",
        "Universal: plot features of interest",
        "One-step preprocessing with prepare_tide()",
        "Interoperability within Bioconductor ecosystem",
        "Common usage scenarios",
        "Session information",
        "References"
      ],
      "created": "2026-04-29 15:58:21",
      "modified": "2026-07-31 18:22:25",
      "commits": 18
    }
  ],
  "_score": 4.7704838094311075,
  "_indexed": true,
  "_nocasepkg": "tideomics",
  "_universes": [
    "bioc",
    "hte123"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.5",
      "date": "2026-10-12T13:51:47.000Z",
      "distro": "resolute",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/01f7081ac19232d1fd27a722dbe0b27130b32bb78ac1cdd6a218c37a9af3be5c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.5",
      "date": "2026-10-12T13:51:57.000Z",
      "distro": "resolute",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/9857ea2910a7a376ba5c23e4d58cd66df4b4e26ea4e2794253568eef101b7f22",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.5",
      "date": "2026-10-12T13:49:26.000Z",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/cc2c07d6845c48157062d7cc1e4baf9fbb1a11fcbf382a713a0861ff8700363b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.5",
      "date": "2026-10-12T13:48:50.000Z",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/34f72035e72f1c36b772b80f87141a93491966a92d4b94363358c8f85db6b30b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.5",
      "date": "2026-10-12T13:51:01.000Z",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/d673e9f0824a01c16e9b4ec1f8d34dd6bc90cdd632a2a3f70aee8434778038c0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.5",
      "date": "2026-10-12T13:49:12.000Z",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/7e9ca5f7bd603035a5d96e1a445fbbe4d0d8ad4158e7aab1fce8772e901f0d31",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.5",
      "date": "2026-10-12T13:49:19.000Z",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/56be0a202b1a054ab369bc3ef44e9e88d79dc8ab3cfb7403e33453a9054ae2de",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.5",
      "date": "2026-10-12T13:49:35.000Z",
      "commit": "ca26312c86214fd3ec8d103e330224611463edd3",
      "fileid": "https://r2.ropensci.org/a0bdcb6caf3b4f076230e88117f40107081ffb9f2f5b3eec7234746ffae55ead",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38256937249"
    }
  ]
}