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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
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see Pigengene.
Infers biological signatures from gene expression data
Bioconductor version: 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")
| R Script | Pigengene: Computing and using eigengenes | |
| 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) (0.5 years) |
| 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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