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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Pigengene")
AuthorHabil Zare, Amir Foroushani, and Rupesh Agrahari
Bioconductor views BiomedicalInformatics Classification Clustering DecisionTree DimensionReduction GeneExpression GraphAndNetwork Microarray Network NetworkInference Normalization PrincipalComponent RNASeq SystemsBiology Transcriptomics
Date of publicationNone
MaintainerHabil Zare <zare@txstate.edu>
LicenseGPL (>=2)
Version1.2.0

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

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

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