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This is the development version of Pigengene; for the stable release version, see Pigengene.

Infers biological signatures from gene expression data

Bioconductor version: Development (3.20)

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, Rupesh Agrahari, Meghan Short, Isha Mehta, Neda Emami, and Sogand Sajedi

Maintainer: Habil Zare <zare at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

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


biocViews BiomedicalInformatics, Classification, Clustering, DecisionTree, DimensionReduction, GeneExpression, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkInference, Normalization, PrincipalComponent, RNASeq, Software, SystemsBiology, Transcriptomics
Version 1.31.2
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>=2)
Depends R (>= 4.0.3), graph, BiocStyle(>= 2.28.0)
Imports bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE
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Suggests>= 3.7.0),>= 3.7.0), biomaRt(>= 2.30.0), knitr, AnnotationDbi, energy
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Source Package Pigengene_1.31.2.tar.gz
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