Package: postNet 1.1.0

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