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.

AuthorHabil Zare, Amir Foroushani, and Rupesh Agrahari
Date of publicationNone
MaintainerHabil Zare <zare@txstate.edu>
LicenseGPL (>=2)
Version1.0.0

View on Bioconductor

Files in this package

Pigengene/DESCRIPTION
Pigengene/NAMESPACE
Pigengene/R
Pigengene/R/add.noise.R Pigengene/R/balance.R Pigengene/R/bn.calculation.R Pigengene/R/bn.calculationS.R Pigengene/R/bn.module.R Pigengene/R/calculate.beta.R Pigengene/R/check.nas.R Pigengene/R/check.pigengene.input.R Pigengene/R/combinedPath.R Pigengene/R/combinedStrength.R Pigengene/R/compact.tree.R Pigengene/R/compute.pigengene.R Pigengene/R/consensus.R Pigengene/R/consensus.thresh.R Pigengene/R/dcor.matrix.R Pigengene/R/draw.bn.R Pigengene/R/draw.bnS.R Pigengene/R/draw.cor.R Pigengene/R/draw.cor.cond.R Pigengene/R/draw.improvement.R Pigengene/R/draw.module.sizes.R Pigengene/R/draw.scores.R Pigengene/R/dummyMaker.R Pigengene/R/enforce.blk.R Pigengene/R/gene.mapping.R Pigengene/R/get.combined.file.R Pigengene/R/get.consensus.files.R Pigengene/R/get.fitted.leaf.R Pigengene/R/get.genes.R Pigengene/R/get.module.data.file.R Pigengene/R/get.sorted.members.R Pigengene/R/get.used.features.R Pigengene/R/getALLRuns.R Pigengene/R/getBN.R Pigengene/R/hu.mouse.R Pigengene/R/indFileName.R Pigengene/R/learn.bn.R Pigengene/R/load.if.R Pigengene/R/make.bn.input.R Pigengene/R/make.decision.tree.R Pigengene/R/make.membership.queue.R Pigengene/R/message.if.R Pigengene/R/module.heatmap.R Pigengene/R/mtrim.R Pigengene/R/noise.analysis.R Pigengene/R/one.step.pigengene.R Pigengene/R/pheatmap.type.R Pigengene/R/plot.pigengene.R Pigengene/R/preds.at.R Pigengene/R/project.eigen.R Pigengene/R/pvalues.manova.R Pigengene/R/rename.nodes.R Pigengene/R/repeat.data.R Pigengene/R/sample.network.R Pigengene/R/save.if.R Pigengene/R/sbatch.R Pigengene/R/scoreCandidates.R Pigengene/R/unique.gene.names.R Pigengene/R/versrem.R Pigengene/R/welch.pvalue.R Pigengene/R/wgcna.one.step.R Pigengene/R/what.is.in.R Pigengene/R/which.cluster.R
Pigengene/build
Pigengene/build/vignette.rds
Pigengene/data
Pigengene/data/aml.RData
Pigengene/data/datalist
Pigengene/data/eigengenes33.RData
Pigengene/data/mds.RData
Pigengene/data/pigengene.RData
Pigengene/inst
Pigengene/inst/CITATION
Pigengene/inst/NEWS.Rd
Pigengene/inst/doc
Pigengene/inst/doc/Pigengene_inference.R
Pigengene/inst/doc/Pigengene_inference.Rnw
Pigengene/inst/doc/Pigengene_inference.pdf
Pigengene/man
Pigengene/man/Pigengene-package.Rd Pigengene/man/aml.Rd Pigengene/man/balance.Rd Pigengene/man/calculate.beta.Rd Pigengene/man/check.pigengene.input.Rd Pigengene/man/compact.tree.Rd Pigengene/man/compute.pigengene.Rd Pigengene/man/dcor.matrix.Rd Pigengene/man/draw.bn.Rd Pigengene/man/eigengenes33.Rd Pigengene/man/gene.mapping.Rd Pigengene/man/get.fitted.leaf.Rd Pigengene/man/get.genes.Rd Pigengene/man/get.used.features.Rd Pigengene/man/learn.bn.Rd Pigengene/man/make.decision.tree.Rd Pigengene/man/mds.Rd Pigengene/man/module.heatmap.Rd Pigengene/man/one.step.pigengene.Rd Pigengene/man/pheatmap.type.Rd Pigengene/man/pigengene-class.Rd Pigengene/man/pigengene.Rd Pigengene/man/plot.pigengene.Rd Pigengene/man/preds.at.Rd Pigengene/man/project.eigen.Rd Pigengene/man/pvalues.manova.Rd Pigengene/man/wgcna.one.step.Rd
Pigengene/vignettes
Pigengene/vignettes/Pigengene_inference.Rnw
Pigengene/vignettes/pigengene.bib

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