codonCalc               Quantify and compare codon or amino acid usage
                        across gene sets
codonUsage              Perform differential codon or amino acid usage
                        analysis between gene sets
contentAnalysis         Calculate nucleotide content of mRNA sequence
                        regions and compare between gene sets
contentMotifs           Detect, quantify, and compare sequence motifs
                        between gene sets
featureIntegration      Feature integration with post-transcriptional
                        network modelling
foldingEnergyAnalysis   Compare mRNA folding energy between gene sets
gageAnalysis            Perform GAGE analysis with a 'postNetData'
                        object
get_signatures          Retrieve gene signatures provided in the
                        postNet
goAnalysis              Perform Gene Ontology Analysis using a
                        'postNetData' object
goDotplot               Produce dot plots with results of GO term
                        enrichment analysis
gseaAnalysis            Perform Gene Set Enrichment Analysis (GSEA)
                        with a 'postNetData' object
gseaPlot                Plot enriched terms from GSEA
humanSignatures         Human gene signatures of translational control
lengthAnalysis          Calculate the length of mRNA sequence regions
                        and compare between gene sets
miRNAanalysis           Perform miRNA target enrichment analysis using
                        a 'postNetData' object
motifAnalysis           De novo motif discovery using STREME and a
                        'postNetData' object
mouseSignatures         Mouse gene signatures of translational control
plotFeaturesMap         Explore mRNA features and regulatory effects
                        using UMAP visualizations
plotSignatures          Analysis of regulation of gene signatures in a
                        'postNetData' object
plotSignatures_ads      Analysis of regulation of gene signatures in an
                        'Anota2seqDataSet' object
postNet-package         Post-transcriptional network modelling with
                        postNet
postNetData-class       S4 Class 'postNetData': Core data container for
                        postNet analyses
postNetExample          An example dataset for demonstrating the usage
                        of postNet functions
postNetStart            Create the data container and inputs for
                        postNet analyses
postNetVignette         An example dataset for demonstrating the
                        workflow of a postNet ananlysis
ptn_background          Accessor for the gene set used as background in
                        a 'postNetData' object
ptn_check_models        Accessor for the feature integration model
                        comparisons in a 'postNetData' object
ptn_codonAnalysis       Accessor for the "codonAnalysis" slot of a
                        'postNetData' object
ptn_codonSelection      Accessor for the "codonSelection" slot of a
                        'postNetData' object
ptn_colours             Accessor for the "colours" slot of a
                        'postNetData' object
ptn_dataIn              Accessor for the "background", "geneList",
                        "effect", and "colours" slots of a
                        'postNetData' object
ptn_effect              Accessor for the regulatory effect measurement
                        from the "effect" slot of a 'postNetData'
                        object
ptn_features            Accessor for the 'features' slot of a
                        'postNetData' object
ptn_GAGE                Accessor for the "GAGE" slot of a 'postNetData'
                        object
ptn_geneID              Accessor for the gene IDs in the "geneID" slot
                        of a 'postNetData' object
ptn_geneList            Accessor for the "geneList" slot of a
                        'postNetData' object
ptn_GO                  Accessor for the "GO" slot of a 'postNetData'
                        object
ptn_GSEA                Accessor for the "GSEA" slot of a 'postNetData'
                        object
ptn_id                  Accessor for the transcript IDs in the "id"
                        slot of a 'postNetData' object
ptn_miRNA_analysis      Accessor for the "miRNA_analysis" slot of a
                        'postNetData' object
ptn_miRNA_to_gene       Accessor for the "miRNA_to_gene" slot of a
                        'postNetData' object
ptn_model               Accessor for the feature integration model
                        slots of a 'postNetData' object
ptn_motifGeneList       Accessor for the de novo motif analysis results
                        for each gene set of interest in a
                        'postNetData' object
ptn_motifSelection      Accessor for the "motifSelection" slot of a
                        'postNetData' object
ptn_networkGraph        Accessor for the 'networkGraph' slot of a
                        'postNetData' object
ptn_selectedFeatures    Accessor for the 'selectedFeatures' slot of a
                        'postNetData' object
ptn_selection           Accessor for the isoform selection parameter
                        from the "selection" slot of a 'postNetData'
                        object
ptn_sequences           Accessor for the reference annotation sequences
                        in the sequence annotation slots of a
                        'postNetData' object
ptn_species             Accessor for the "species" slot of a
                        'postNetData' object
ptn_version             Accessor for the RefSeq annotation release
                        version from the "version" slot of a
                        'postNetData' object
rfPred                  Predict post-transcriptional regulation using
                        trained random forest models
signaturesHeatmap       Generate heatmaps to evaluate the regulation of
                        gene signatures in a 'postNetData' object
signCalc                Create gene signatures for use in feature
                        integration analysis
slopeFilt               Filtering 'anota2seq' analysis results
                        according to slopes for use in GSEA, GAGE, and
                        GO term analyses
uorfAnalysis            Detect and quantify upstream open reading
                        frames (uORFs)
