{
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  "Package": "GRaNIE",
  "Title": "GRaNIE: Reconstruction cell type specific gene regulatory\nnetworks including enhancers using single-cell or bulk\nchromatin accessibility and RNA-seq data",
  "Version": "1.17.0",
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  "Authors@R": "c(person(\"Christian\", \"Arnold\", email =\n\"chrarnold@web.de\", role = c(\"cre\",\"aut\")),\nperson(\"Judith\", \"Zaugg\", email =\n\"judith.zaugg@embl.de\", role = c(\"aut\")),\nperson(\"Rim\", \"Moussa\", email =\n\"rim.moussa01@gmail.com\", role = \"aut\"),\nperson(\"Armando\", \"Reyes-Palomares\", email =\n\"armandorp@gmail.com\", role = \"ctb\"),\nperson(\"Giovanni\", \"Palla\", email =\n\"giov.pll@gmail.com\", role = \"ctb\"),\nperson(\"Maksim\", \"Kholmatov\", email =\n\"maksim.kholmatov@embl.de\", role = \"ctb\"))",
  "Description": "Genetic variants associated with diseases often affect\nnon-coding regions, thus likely having a regulatory role. To\nunderstand the effects of genetic variants in these regulatory\nregions, identifying genes that are modulated by specific\nregulatory elements (REs) is crucial. The effect of gene\nregulatory elements, such as enhancers, is often cell-type\nspecific, likely because the combinations of transcription\nfactors (TFs) that are regulating a given enhancer have\ncell-type specific activity. This TF activity can be quantified\nwith existing tools such as diffTF and captures differences in\nbinding of a TF in open chromatin regions. Collectively, this\nforms a gene regulatory network (GRN) with cell-type and\ndata-specific TF-RE and RE-gene links. Here, we reconstruct\nsuch a GRN using single-cell or bulk RNAseq and open chromatin\n(e.g., using ATACseq or ChIPseq for open chromatin marks) and\noptionally (Capture) Hi-C data. Our network contains different\ntypes of links, connecting TFs to regulatory elements, the\nlatter of which is connected to genes in the vicinity or within\nthe same chromatin domain (TAD). We use a statistical framework\nto assign empirical FDRs and weights to all links using a\npermutation-based approach.",
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  "biocViews": "Software, GeneExpression, GeneRegulation, NetworkInference,\nGeneSetEnrichment, BiomedicalInformatics, Genetics,\nTranscriptomics, ATACSeq, RNASeq, GraphAndNetwork, Regression,\nTranscription, ChIPSeq",
  "License": "Artistic-2.0",
  "URL": "https://grp-zaugg.embl-community.io/GRaNIE",
  "BugReports": "https://git.embl.de/grp-zaugg/GRaNIE/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:24 UTC",
  "RemoteUrl": "https://github.com/bioc/GRaNIE",
  "RemoteRef": "HEAD",
  "RemoteSha": "1bfee582f100e1b394360d045b4f9cfe28277992",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-11 15:13:46 UTC",
    "User": "root"
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  "Author": "Christian Arnold [cre, aut],\nJudith Zaugg [aut],\nRim Moussa [aut],\nArmando Reyes-Palomares [ctb],\nGiovanni Palla [ctb],\nMaksim Kholmatov [ctb]",
  "Maintainer": "Christian Arnold <chrarnold@web.de>",
  "_user": "bioc",
  "_type": "src",
  "_file": "GRaNIE_1.17.0.tar.gz",
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  "_expires": "2027-01-19T15:34:46.000Z",
  "_created": "2026-10-11T15:13:46.000Z",
  "_published": "2026-10-11T15:34:47.946Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38149236854",
  "_status": "failure",
  "_host": "GitHub-Actions",
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    "note": 17
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  "_upstream": "https://github.com/bioc/GRaNIE",
  "_commit": {
    "id": "1bfee582f100e1b394360d045b4f9cfe28277992",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381104
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    "plotCommunitiesEnrichment",
    "plotCommunitiesStats",
    "plotCorrelations",
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    "plotDiagnosticPlots_TFPeaks",
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      "page": "add_featureVariation",
      "title": "Quantify and interpret multiple sources of biological and technical variation for features (TFs, peaks, and genes) in a 'GRN' object",
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      "title": "Add peak-gene connections to a 'GRN' object",
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      "title": "Add TF-peak connections to a 'GRN' object",
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      "title": "Add data to a 'GRN' object.",
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      "page": "addData_TFActivity",
      "title": "Add TF activity data to GRN object using a simplified procedure for estimating it. EXPERIMENTAL.",
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      "title": "Add SNP data to a 'GRN' object and associate SNPs to peaks.",
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      "title": "Add TFBS to a 'GRN' object.",
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      "title": "Run the activator-repressor classification for the TFs for a 'GRN' object",
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      "title": "Builds a graph out of a set of connections",
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      "title": "Run an enrichment analysis for the genes in each community in the filtered 'GRN' object",
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      "title": "Generate graph communities and their summarizing statistics",
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      "title": "Run an enrichment analysis for the set of genes connected to a particular TF or sets of TFs in the filtered 'GRN' object",
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      "title": "Optional convenience function to delete intermediate data from the function 'AR_classification_wrapper' and summary statistics that may occupy a lot of space",
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      "title": "Filter connections for subsequent visualization with `visualizeGRN()` from the filtered eGRN",
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      "title": "Filter TF-peaks and peak-gene connections and combine them to TF-peak-gene connections to construct an eGRN.",
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      "title": "Generate a summary for the number of connections for different filtering criteria for a 'GRN' object.",
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      "title": "Get counts for the various data defined in a 'GRN' object",
      "topics": [
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      "title": "Extract connections or links from a 'GRN' object as a data frame.",
      "topics": [
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      "title": "Summarize a 'GRN' object to a named list for comparison with other 'GRN' objects.",
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      "title": "Retrieve parameters for previously used function calls and general parameters for a 'GRN' object.",
      "topics": [
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      "page": "getTopNodes",
      "title": "Retrieve the top nodes (TFs or genes) with respect to either degree or Eigenvector centrality in the filtered 'GRN' object.",
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      "page": "GRaNIE",
      "title": "*GRaNIE* (*G*ene *R*egul*a*tory *N*etwork *I*nference including *E*nhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information)",
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        "GRaNIE"
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      "page": "GRN-class",
      "title": "Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (*eGRNs*)",
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      "page": "importTFData",
      "title": "Import externally derived TF Activity data. EXPERIMENTAL.",
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      "page": "initializeGRN",
      "title": "Create and initialize an empty 'GRN' object.",
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      "title": "Load example GRN dataset",
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      "page": "nGenes",
      "title": "Get the number of genes for a 'GRN' object.",
      "topics": [
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        "nGenes"
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    },
    {
      "page": "nPeaks",
      "title": "Get the number of peaks for a 'GRN' object.",
      "topics": [
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        "peaks"
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      "page": "nTFs",
      "title": "Get the number of TFs for a 'GRN' object.",
      "topics": [
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      "title": "Overlap peaks and TFBS for a 'GRN' object",
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      "title": "Perform all network-related statistical and descriptive analyses, including community and enrichment analyses. See the functions it executes in the @seealso section below.",
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      "page": "plot_stats_connectionSummary",
      "title": "Plot various network connectivity summaries for a 'GRN' object",
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      "title": "Plot community-based enrichment results for a filtered 'GRN' object",
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      "title": "Plot general structure & connectivity statistics for each community in a filtered 'GRN'",
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      "page": "plotCorrelations",
      "title": "Plot scatter plots of the underlying count data for either TF-peak, peak-gene or TF-gene pairs for a 'GRN' object",
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      "page": "plotDiagnosticPlots_peakGene",
      "title": "Plot diagnostic plots for peak-gene connections for a 'GRN' object",
      "topics": [
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    {
      "page": "plotDiagnosticPlots_TFPeaks",
      "title": "Plot diagnostic plots for TF-peak connections for a 'GRN' object",
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      "page": "plotDiagnosticPlots_TFPeaks_GC",
      "title": "Plot GC-specific diagnostic plots for TF-peak connections for a 'GRN' object",
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    {
      "page": "plotGeneralEnrichment",
      "title": "Plot the general enrichement results",
      "topics": [
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      "page": "plotGeneralGraphStats",
      "title": "Plot general structure and connectivity statistics for a filtered 'GRN' object",
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      "title": "Produce a PCA plot of the data from a 'GRN' object",
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      "title": "Plot TF-based GO enrichment results",
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    {
      "page": "visualizeGRN",
      "title": "Visualize a filtered eGRN in a flexible manner.",
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