Pigengene: Infers biological signatures from gene expression data

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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.

Author
Habil Zare, Amir Foroushani, and Rupesh Agrahari
Date of publication
None
Maintainer
Habil Zare <zare@txstate.edu>
License
GPL (>=2)
Version
1.0.0

View on Bioconductor

Man pages

aml
AML gene expression profile
balance
Balances the number of sampels
calculate.beta
Estimates an appropriate power value
check.pigengene.input
Quality check on the imput
compact.tree
Reduces the number of genes in a decision tree
compute.pigengene
Computes the eigengenes
dcor.matrix
Computes distance correlation for give matrix
draw.bn
Draws a Bayesian network
eigengenes33
Eigengenes of 33 modules
gene.mapping
Maps gene IDs
get.fitted.leaf
Returs the leaf for each sample
get.genes
List the (most relevant) genes for a decision tree.
get.used.features
Return the features used in a tree
learn.bn
Learns a Bayesian network
make.decision.tree
Creates a decision tree to classify samples using the...
mds
MDS gene expression profile
module.heatmap
Plots heatmaps for modules
one.step.pigengene
Runs the entire Pigengene pipeline
pheatmap.type
Plots heatmap with clustering only within types.
pigengene
An object of class 'Pigengene'
pigengene-class
The pigengene class
Pigengene-package
Infers robust biological signatures from gene expression data
plot.pigengene
Plots and saves a 'pigengene' object
preds.at
Prediction using a possibly compacted tree
project.eigen
Infers eigengenes for given expression data
pvalues.manova
Computes pvalues for multi-class differential expression
wgcna.one.step
Module identification

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