{
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  "Package": "cTRAP",
  "Title": "Identification of candidate causal perturbations from\ndifferential gene expression data",
  "Version": "1.31.0",
  "Authors@R": "c(\nperson(c(\"Bernardo\", \"P.\"), \"de Almeida\", role=\"aut\"),\nperson(\"Nuno\", \"Saraiva-Agostinho\",\nemail=\"nunodanielagostinho@gmail.com\", role=c(\"aut\", \"cre\")),\nperson(c(\"Nuno\", \"L.\"), \"Barbosa-Morais\", role=c(\"aut\", \"led\")))",
  "Description": "Compare differential gene expression results with those\nfrom known cellular perturbations (such as gene knock-down,\noverexpression or small molecules) derived from the\nConnectivity Map. Such analyses allow not only to infer the\nmolecular causes of the observed difference in gene expression\nbut also to identify small molecules that could drive or revert\nspecific transcriptomic alterations.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:00 UTC",
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  "Author": "Bernardo P. de Almeida [aut],\nNuno Saraiva-Agostinho [aut, cre],\nNuno L. Barbosa-Morais [aut, led]",
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      "title": "Cross Tabulation and Table Creation",
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        "functions related with the ranking of CMap perturbations"
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      "title": "Convert ENSEMBL gene identifiers to gene symbols",
      "topics": [
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      "page": "convertGeneIdentifiers",
      "title": "Convert gene identifiers",
      "concept": [
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      "page": "cTRAP",
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        "cTRAP"
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      "title": "List available conditions in CMap datasets",
      "concept": [
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      "title": "Get CMap perturbation types",
      "concept": [
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      "topics": [
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      "title": "Load CMap data via a visual interface",
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      "title": "Load differential expression data via a visual interface",
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      "source": "cTRAP.Rmd",
      "filename": "cTRAP.html",
      "title": "cTRAP: identifying candidate causal perturbations from differential gene expression data",
      "author": "Bernardo P. de Almeida & Nuno Saraiva-Agostinho",
      "engine": "knitr::rmarkdown",
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        "Introduction",
        "Getting started",
        "Load ENCODE RNA-seq data and perform differential gene expression analysis",
        "Load CMap perturbation data",
        "Comparison with CMap perturbations",
        "Information on perturbations",
        "Relationship plots",
        "Predict targeting drugs",
        "Molecular descriptor enrichment analysis",
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      "modified": "2024-03-27 12:10:30",
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