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

Functions

aml Man page
balance Man page
calculate.beta Man page
check.pigengene.input Man page
compact.tree Man page
compute.pigengene Man page
dcor.matrix Man page
draw.bn Man page
eigengenes33 Man page
gene.mapping Man page
get.fitted.leaf Man page
get.genes Man page
get.used.features Man page
learn.bn Man page
make.decision.tree Man page
mds Man page
module.heatmap Man page
one.step.pigengene Man page
pheatmap.type Man page
pigengene Man page
pigengene-class Man page
Pigengene-package Man page
plot.pigengene Man page
plot, pigengene-method Man page
preds.at Man page
project.eigen Man page
pvalues.manova Man page
wgcna.one.step Man page

Files

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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