Package: Pigengene
Type: Package
Title: Infers biological signatures from gene expression data
Version: 1.39.0
Date: 2016-03-31
Author: Habil Zare, Amir Foroushani, Rupesh Agrahari, Meghan Short,
        Isha Mehta, Neda Emami, and Sogand Sajedi
Maintainer: Habil Zare <zare@u.washington.edu>
biocViews: GeneExpression, RNASeq, NetworkInference, Network,
        GraphAndNetwork, BiomedicalInformatics, SystemsBiology,
        Transcriptomics, Classification, Clustering, DecisionTree,
        DimensionReduction, PrincipalComponent, Microarray,
        Normalization, ImmunoOncology
Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0)
Description: 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.
License: GPL (>=2)
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
Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>=
        2.30.0), knitr, AnnotationDbi, energy
VignetteBuilder: knitr
NeedsCompilation: no
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:43:36 UTC
RemoteUrl: https://github.com/bioc/Pigengene
RemoteRef: HEAD
RemoteSha: cc08c7aba6154b530e62af509efa2f5f7afb239c
Packaged: 2026-07-04 00:34:34 UTC; root
Built: R 4.6.1; ; 2026-07-04 00:37:53 UTC; windows
