To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Pigengene")

In most cases, you don't need to download the package archive at all.

Pigengene

 

   

Infers biological signatures from gene expression data

Bioconductor version: Release (3.4)

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

Maintainer: Habil Zare <zare at txstate.edu>

Citation (from within R, enter citation("Pigengene")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Pigengene")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Pigengene")

 

PDF R Script Pigengene: Computing and using eigengenes
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, Classification, Clustering, DecisionTree, DimensionReduction, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkInference, Normalization, PrincipalComponent, RNASeq, Software, SystemsBiology, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.4 (R-3.3) (< 6 months)
License GPL (>=2)
Depends R (>= 3.3.0), graph
Imports bnlearn, C50, MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8)
LinkingTo
Suggests org.Hs.eg.db, org.Mm.eg.db, biomaRt, knitr, BiocStyle, AnnotationDbi, energy
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source Pigengene_1.0.0.tar.gz
Windows Binary Pigengene_1.0.0.zip
Mac OS X 10.9 (Mavericks) Pigengene_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Pigengene/tree/release-3.4
Package Short Url http://bioconductor.org/packages/Pigengene/
Package Downloads Report Download Stats

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