Post-transcriptional network modeling

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Documentation for package ‘postNet’ version 0.99.9

• 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)