Package: Pigengene 1.33.0

Habil Zare

Pigengene: Infers biological signatures from gene expression data

Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.

Authors:Habil Zare, Amir Foroushani, Rupesh Agrahari, Meghan Short, Isha Mehta, Neda Emami, and Sogand Sajedi

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Pigengene.pdf |Pigengene.html✨
Pigengene/json (API)
NEWS

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

Peer review:

Datasets:
  • aml - AML gene expression profile
  • eigengenes33 - Eigengenes of 33 modules
  • mds - MDS gene expression profile
  • pigengene - An object of class 'Pigengene'

On BioConductor:Pigengene-1.33.0(bioc 3.21)Pigengene-1.32.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressionrnaseqnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdecisiontreedimensionreductionprincipalcomponentmicroarraynormalizationimmunooncology

4.56 score 1 packages 10 scripts 242 downloads 4 mentions 29 exports 175 dependencies

Last updated 2 months agofrom:25bba85b6c. Checks:OK: 1 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024

Exports:apply.filterbalancecalculate.betacheck.nascheck.pigengene.inputcombine.networkscompact.treecompute.pigengenedcor.matrixdetermine.modulesdraw.bngene.mappingget.enriched.pwget.fitted.leafget.genesget.used.featureslearn.bnmake.decision.treemake.filtermessage.ifmodule.heatmapone.step.pigengenepheatmap.typeplot.pigengenepreds.atproject.eigenpvalues.manovasave.ifwgcna.one.step

Dependencies:AnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStyleBiostringsbitbit64blobbnlearnbookdownbslibC50cachemcheckmatecliclusterclusterProfilercodetoolscolorspacecowplotcpp11crayonCubistcurldata.tableDBIdigestdoParallelDOSEdplyrdynamicTreeCutenrichplotevaluatefansifarverfastclusterfastmapfastmatchfgseafontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgdatagenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtangleggtreeglueGO.dbGOSemSimgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphimputeinumIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallibcoinlifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetopensslopenxlsxpartykitpatchworkpheatmappillarpkgconfigplogrplyrpngpolyclippreprocessCorepurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreactome.dbReactomePAreshape2RgraphvizrlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalesscatterpiesnowstringistringrsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunXVectoryamlyulab.utilszipzlibbioc

Pigengene: Computing and using eigengenes

Rendered fromPigengene_inference.Rnwusingknitr::knitron Dec 18 2024.

Last update: 2021-10-14
Started: 2016-05-26

Readme and manuals

Help Manual

Help pageTopics
Infers robust biological signatures from gene expression dataPigengene-package Pigengene
AML gene expression profileaml
Applies a given filter on the dataapply.filter
Balances the number of samplesbalance
Estimates an appropriate power valuecalculate.beta
Removes 'NA's from a data matrixcheck.nas
Quality check on the imputcheck.pigengene.input
Combines two or more networkscombine.networks
Reduces the number of genes in a decision treecompact.tree
Computes the eigengenescompute.pigengene
Computes distance correlation for give matrixdcor.matrix
Identifies modules of the networkdetermine.modules
Draws a Bayesian networkdraw.bn
Eigengenes of 33 moduleseigengenes33
Maps gene IDsgene.mapping
Performs pathway over representation analysisget.enriched.pw
Returs the leaf for each sampleget.fitted.leaf
List the (most relevant) genes for a decision tree.get.genes
Return the features used in a treeget.used.features
Learns a Bayesian networklearn.bn
Creates a decision tree to classify samples using the eigengenes valuesmake.decision.tree
Computes the filter based on a similarity networkmake.filter
MDS gene expression profilemds
Conditional messaging.message.if
Plots heatmaps for modulesmodule.heatmap
Runs the entire Pigengene pipelineone.step.pigengene
Plots heatmap with clustering only within types.pheatmap.type
An object of class 'Pigengene'pigengene
The pigengene classpigengene-class plot, pigengene-method
Plots and saves a 'pigengene' objectplot.pigengene
Prediction using a possibly compacted treepreds.at
Infers eigengenes for given expression dataproject.eigen
Computes pvalues for multi-class differential expressionpvalues.manova
Saves an object verbosely.save.if
Module identificationwgcna.one.step