# Post-transcriptional network modeling

## Documentation for package ‘postNet’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

postNet-package | Post-transcriptional network modelling with postNet
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 | 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_background-method | 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_codonAnalysis-method | Accessor for the "codonAnalysis" slot of a 'postNetData' object
ptn_codonSelection | Accessor for the "codonSelection" slot of a 'postNetData' object
ptn_codonSelection-method | Accessor for the "codonSelection" slot of a 'postNetData' object
ptn_colours | Accessor for the "colours" slot of a 'postNetData' object
ptn_colours-method | 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_dataIn-method | 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_effect-method | 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_features-method | 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_geneID-method | 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_geneList-method | 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_id-method | 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_motifGeneList-method | 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_motifSelection-method | Accessor for the "motifSelection" slot of a 'postNetData' object
ptn_networkGraph | Accessor for the 'networkGraph' slot of a 'postNetData' object
ptn_networkGraph-method | 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_selection-method | 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_sequences-method | 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_species-method | 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
ptn_version-method | 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)