Package: postNet 1.0.0

Krzysztof Szkop

postNet: Post-transcriptional network modeling

A tool that enables in silico identification, integration, and modeling of mRNA features that influence post-transcriptional regulation of gene expression at a transcriptome-wide scale.

Authors:Krzysztof Szkop [aut, cre], Kathleen Watt [aut], Ola Larsson [aut]

postNet_1.0.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
postNet/json (API)
NEWS

# Install 'postNet' in R:
install.packages('postNet', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kszkop/postnet/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • humanSignatures - Human gene signatures of translational control
  • mouseSignatures - Mouse gene signatures of translational control
  • postNetExample - An example dataset for demonstrating the usage of postNet functions
  • postNetVignette - An example dataset for demonstrating the workflow of a postNet ananlysis

On BioConductor:postNet-1.1.0(bioc 3.24)postNet-1.0.0(bioc 3.23)

geneexpressiongeneregulationtranscriptomicsriboseqrnaseqsequencingannotationnetworkfeatureextractioncpp

5.13 score 276 downloads 49 exports 256 dependencies

Last updated from:7f826932bc (on RELEASE_3_23). Checks:1 NOTE, 13 OK. Indexed: no.

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Exports:codonCalccodonUsagecontentAnalysiscontentMotifsfeatureIntegrationfoldingEnergyAnalysisgageAnalysisget_signaturesgoAnalysisgoDotplotgseaAnalysisgseaPlotlengthAnalysismiRNAanalysismotifAnalysisplotFeaturesMapplotSignaturesplotSignatures_adspostNetStartptn_backgroundptn_check_modelsptn_codonAnalysisptn_codonSelectionptn_coloursptn_dataInptn_effectptn_featuresptn_GAGEptn_geneIDptn_geneListptn_GOptn_GSEAptn_idptn_miRNA_analysisptn_miRNA_to_geneptn_modelptn_motifGeneListptn_motifSelectionptn_networkGraphptn_selectedFeaturesptn_selectionptn_sequencesptn_speciesptn_versionrfPredsignaturesHeatmapsignCalcslopeFiltuorfAnalysis

Dependencies:abindade4aisdkannotateAnnotationDbiAnnotationHubanota2seqapeaplotaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBorutabriobslibcachemcallrcaretcaToolsclassclicliprclockclusterclusterProfilercmdfuncodetoolscowplotcpp11crayoncredentialscurldata.tableDBIdbplyrDelayedArraydescDESeq2diagramdiffobjdigestDOSEdplyre1071edgeRenrichitenrichplotevaluateExperimentHubfarverfastmapfastmatchfgseafilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfrufsfutile.loggerfutile.optionsfuturefuture.applygagegdtoolsgenericsGenomicRangesgertggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreegitcredsglobalsglueGO.dbGOSemSimgowergplotsgraphgridExtragridGraphicsGSEABasegsongtablegtoolshardhatherehighrhmshtmltoolshtmlwidgetshttrhttr2igraphiniipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelavalazyevallifecyclelimmalistenvlocfitlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemesmemoisemimeModelMetricsmsigdbmulttestnlmennetnumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbparallellypatchworkpillarpixmappkgbuildpkgconfigpkgloadplotrixplyrpngpolyclippraiseprettyunitspROCprocessxprodlimprogressprogressrproxypspurrrqvalueR.methodsS3R.ooR.utilsR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppThreadRcppTOMLreadrrecipesreshape2reticulaterlangrmarkdownROCRrpartrprojrootRSpectraRSQLiterstudioapirvestS4ArraysS4VectorsS7sassscalesscatterpiesegmentedselectrSeqinfoseqinrshapesmsnowspSparseArraysparsevctrsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattibbletidydrtidyrtidyselecttidytreetimechangetimeDatetinytextreeiotweenrtzdbumapuniversalmotifusethisutf8vctrsvioplotviridisLitevroomwaldowhiskerwithrWriteXLSxfunXMLxml2xtableXVectoryamlyulab.utilszipzoo

Post-transcriptional network modelling with postNet

Krzysztof J. Szkop, Kathleen Watt, Ola Larsson

Rendered frompostNet.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-11
Started: 2025-07-11

Readme and manuals

Help Manual

Help pageTopics
Post-transcriptional network modelling with postNetpostNet-package postNet
Quantify and compare codon or amino acid usage across gene setscodonCalc
Perform differential codon or amino acid usage analysis between gene setscodonUsage
Calculate nucleotide content of mRNA sequence regions and compare between gene setscontentAnalysis
Detect, quantify, and compare sequence motifs between gene setscontentMotifs
Feature integration with post-transcriptional network modellingfeatureIntegration
Compare mRNA folding energy between gene setsfoldingEnergyAnalysis
Perform GAGE analysis with a 'postNetData' objectgageAnalysis
Retrieve gene signatures provided in the postNetget_signatures
Perform Gene Ontology Analysis using a 'postNetData' objectgoAnalysis
Produce dot plots with results of GO term enrichment analysisgoDotplot
Perform Gene Set Enrichment Analysis (GSEA) with a 'postNetData' objectgseaAnalysis
Plot enriched terms from GSEAgseaPlot
Human gene signatures of translational controlhumanSignatures
Calculate the length of mRNA sequence regions and compare between gene setslengthAnalysis
Perform miRNA target enrichment analysis using a 'postNetData' objectmiRNAanalysis
De novo motif discovery using STREME and a 'postNetData' objectmotifAnalysis
Mouse gene signatures of translational controlmouseSignatures
Explore mRNA features and regulatory effects using UMAP visualizationsplotFeaturesMap
Analysis of regulation of gene signatures in a 'postNetData' objectplotSignatures
Analysis of regulation of gene signatures in an 'Anota2seqDataSet' objectplotSignatures_ads
S4 Class 'postNetData': Core data container for postNet analysespostNetData-class
An example dataset for demonstrating the usage of postNet functionspostNetExample
Create the data container and inputs for postNet analysespostNetStart
An example dataset for demonstrating the workflow of a postNet ananlysispostNetVignette
Accessor for the gene set used as background in a 'postNetData' objectptn_background ptn_background,postNetData-method
Accessor for the feature integration model comparisons in a 'postNetData' objectptn_check_models
Accessor for the "codonAnalysis" slot of a 'postNetData' objectptn_codonAnalysis ptn_codonAnalysis,postNetData-method
Accessor for the "codonSelection" slot of a 'postNetData' objectptn_codonSelection ptn_codonSelection,postNetData-method
Accessor for the "colours" slot of a 'postNetData' objectptn_colours ptn_colours,postNetData-method
Accessor for the "background", "geneList", "effect", and "colours" slots of a 'postNetData' objectptn_dataIn ptn_dataIn,postNetData-method
Accessor for the regulatory effect measurement from the "effect" slot of a 'postNetData' objectptn_effect ptn_effect,postNetData-method
Accessor for the 'features' slot of a 'postNetData' objectptn_features ptn_features,postNetData-method
Accessor for the "GAGE" slot of a 'postNetData' objectptn_GAGE
Accessor for the gene IDs in the "geneID" slot of a 'postNetData' objectptn_geneID ptn_geneID,postNetData-method
Accessor for the "geneList" slot of a 'postNetData' objectptn_geneList ptn_geneList,postNetData-method
Accessor for the "GO" slot of a 'postNetData' objectptn_GO
Accessor for the "GSEA" slot of a 'postNetData' objectptn_GSEA
Accessor for the transcript IDs in the "id" slot of a 'postNetData' objectptn_id ptn_id,postNetData-method
Accessor for the "miRNA_analysis" slot of a 'postNetData' objectptn_miRNA_analysis
Accessor for the "miRNA_to_gene" slot of a 'postNetData' objectptn_miRNA_to_gene
Accessor for the feature integration model slots of a 'postNetData' objectptn_model
Accessor for the de novo motif analysis results for each gene set of interest in a 'postNetData' objectptn_motifGeneList ptn_motifGeneList,postNetData-method
Accessor for the "motifSelection" slot of a 'postNetData' objectptn_motifSelection ptn_motifSelection,postNetData-method
Accessor for the 'networkGraph' slot of a 'postNetData' objectptn_networkGraph ptn_networkGraph,postNetData-method
Accessor for the 'selectedFeatures' slot of a 'postNetData' objectptn_selectedFeatures
Accessor for the isoform selection parameter from the "selection" slot of a 'postNetData' objectptn_selection ptn_selection,postNetData-method
Accessor for the reference annotation sequences in the sequence annotation slots of a 'postNetData' objectptn_sequences ptn_sequences,postNetData-method
Accessor for the "species" slot of a 'postNetData' objectptn_species ptn_species,postNetData-method
Accessor for the RefSeq annotation release version from the "version" slot of a 'postNetData' objectptn_version ptn_version,postNetData-method
Predict post-transcriptional regulation using trained random forest modelsrfPred
Generate heatmaps to evaluate the regulation of gene signatures in a 'postNetData' objectsignaturesHeatmap
Create gene signatures for use in feature integration analysissignCalc
Filtering 'anota2seq' analysis results according to slopes for use in GSEA, GAGE, and GO term analysesslopeFilt
Detect and quantify upstream open reading frames (uORFs)uorfAnalysis