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      "title": "Accessor for the \"background\", \"geneList\", \"effect\", and \"colours\" slots of a 'postNetData' object",
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      "page": "ptn_model",
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      "title": "Accessor for the de novo motif analysis results for each gene set of interest in a 'postNetData' object",
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      ]
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    {
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      ]
    },
    {
      "page": "ptn_networkGraph",
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      ]
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    {
      "page": "ptn_selectedFeatures",
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      "page": "ptn_selection",
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      ]
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    {
      "page": "ptn_sequences",
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      "topics": [
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      ]
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      ]
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    {
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      "title": "Accessor for the RefSeq annotation release version from the \"version\" slot of a 'postNetData' object",
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      ]
    },
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      "page": "rfPred",
      "title": "Predict post-transcriptional regulation using trained random forest models",
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        "rfPred"
      ]
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      "page": "signaturesHeatmap",
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      ]
    },
    {
      "page": "uorfAnalysis",
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        "uorfAnalysis"
      ]
    }
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      "source": "postNet.Rmd",
      "filename": "postNet.html",
      "title": "Post-transcriptional network modelling with postNet",
      "author": "Krzysztof J. Szkop, Kathleen Watt, Ola Larsson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Workflow",
        "Getting started",
        "Setting up a postNet analysis",
        "Initializing a postNetData object using custom gene lists",
        "Initializing a postNetData object using an Anota2seqDataSet object",
        "Reference sequence annotations",
        "Loading in-built reference sequence annotations",
        "Retrieving or constructing reference sequence annotations from the NCBI RefSeq database",
        "Using custom reference sequence annotations",
        "Selecting transcript isoforms",
        "Adjusting UTR sequence annotations",
        "Analysis of mRNA sequence features",
        "Statistical comparisons, selecting sequence sub-regions, and plotting options",
        "Length of sequence regions",
        "Nucleotide content",
        "Folding energy",
        "Upstream open reading frames",
        "Motif discovery using STREME",
        "Motif enumeration",
        "Codon and amino acid usage",
        "Generating a codon and amino acid count and frequency table",
        "Codon usage indexes",
        "Selecting enriched or depleted codons or amino acids",
        "Enumerating selected codons or amino acids",
        "Modelling and network analysis of post-transcriptional regulation",
        "Selecting features for modelling",
        "Cis-acting features",
        "Trans-acting features",
        "Creating custom features",
        "Highly correlated variables and general features",
        "Creating the feature list",
        "Feature integration with forward stepwise linear regression",
        "Phase 1: Univariate models",
        "Phase 2: Stepwise regression model (omnibus)",
        "Phase 3: Adjusted model",
        "Feature correlations",
        "Running feature integration with forward stepwise linear regression",
        "Network visualizations",
        "Feature integration with Random Forest classification",
        "Pre-modelling and feature selection",
        "Final modelling",
        "Running feature integration with Random Forest classification",
        "Individual feature visualizations",
        "Predicting post-transcriptional regulation in new datasets",
        "Visualizing relationships between features and regulatory effects with UMAP",
        "Plotting UMAPs",
        "Functional enrichment and threshold-independent signature analyses with postNet",
        "Slope filtering when using an Anota2seqDataSet object",
        "Performing GSEA with a postNetData object",
        "GAGE analysis with a postNetData object",
        "microRNA target enrichment analysis with a postNetData object",
        "GO term analysis with a postNetData object",
        "Analysis of gene signatures using eCDFs",
        "Assessing gene signature regulation using the gene list workflow",
        "Assessing gene signature regulation from the anota2seq object workflow",
        "Generating gene signature regulation heatmaps",
        "Citing postNet and implemented tools",
        "Session info",
        "References"
      ],
      "created": "2025-07-11 09:54:59",
      "modified": "2026-03-11 13:01:01",
      "commits": 95
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