Package: netZooR
Type: Package
Title: A Menagerie of Methods for the Inference and Analysis of Gene
        Regulatory Networks
Version: 1.14.1
Date: 2026-02-27
Authors@R: c(person("Tara", "Eicher",
			email = "teicher@hsph.harvard.edu", role = c("aut"), comment = c(ORCID = "0000-0003-1809-4458")),
	     person("Marouen", "Ben Guebila",
                        email = "marouen.b.guebila@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5934-966X")),
	     person("Tian", "Wang", 
			email = "tian.wang@bc.edu", role = c("aut"), comment = c(ORCID = "0000-0002-2767-3243")),
	     person("John", "Platig",
			email="john.platig@channing.harvard.edu", role="aut"),
	     person("Marieke", "Kuijjer",
			email = "marieke.kuijjer@ncmm.uio.no", role = "aut", comment = c(ORCID = "0000-0001-6280-3130")),
	     person("Megha", "Padi",
			email = "mpadi@email.arizona.edu", role = "aut", comment = c(ORCID = "0000-0002-3446-4562")),
	     person("Rebekka", "Burkholz",
			email = "rburkholz@hsph.harvard.edu",role = "aut"),
             person("Des", "Weighill",
                        email = "",role = "aut", comment = c(ORCID = "0000-0003-4979-5871")),
             person("Chen", "Chen",
                        email = "",role = "aut", comment = c(ORCID = "0000-0002-8042-7201")),
             person("Kate", "Shutta",
                        email = "",role = "aut", comment = c(ORCID = "0000-0003-0402-3771")))
Description: Unifies the implementations of several Network Zoo methods
        (netzoo, netzoo.github.io) into a single package by creating
        interfaces between network inference and network analysis
        methods. Currently, the package has 3 methods for network
        inference including PANDA and its optimized implementation
        OTTER (network reconstruction using multiple lines of
        biological evidence), LIONESS (single-sample network
        inference), and EGRET (genotype-specific networks). Network
        analysis methods include CONDOR (community detection), ALPACA
        (differential community detection), CRANE (significance
        estimation of differential modules), MONSTER (estimation of
        network transition states). In addition, YARN allows to process
        gene expression data for tissue-specific analyses and SAMBAR
        infers missing mutation data based on pathway information.
Depends: R (>= 4.2.0), igraph, reticulate, pandaR, Biobase
biocViews: GeneExpression, GeneRegulation, GraphAndNetwork, Microarray,
        Network, NetworkInference, Transcription
Imports: matrixStats, Matrix, stats, utils, methods, graphics,
        parallel, doParallel, foreach, reshape, MASS, data.table
License: GPL-3
Encoding: UTF-8
LazyData: false
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown, viridisLite,
        STRINGdb, GOstats, AnnotationDbi, GO.db, org.Hs.eg.db,
        matrixTests, gplots, nnet, vegan, reshape2, penalized, ggplot2,
        ggdendro, grid, assertthat, tidyr, dplyr, GeneNet, loo,
        rARPACK, corpcor, biomaRt, downloader, edgeR, limma,
        preprocessCore, readr, RColorBrewer, quantro, fgsea
Remotes: jnpaulson/pandaR
VignetteBuilder: knitr
RoxygenNote: 7.3.3
BugReports: https://github.com/netZoo/netZooR/issues
URL: https://github.com/netZoo/netZooR, https://netzoo.github.io/
PackageStatus: Deprecated
Config/pak/sysreqs: libglpk-dev libpng-dev libxml2-dev python3
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-02-27 23:02:44 UTC
RemoteUrl: https://github.com/bioc/netZooR
RemoteRef: RELEASE_3_22
RemoteSha: 42aeb7f30efadec2a0f3e9e2980bac42f0fb6749
NeedsCompilation: no
Packaged: 2026-02-28 04:00:04 UTC; root
Author: Tara Eicher [aut] (ORCID: <https://orcid.org/0000-0003-1809-4458>),
  Marouen Ben Guebila [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5934-966X>),
  Tian Wang [aut] (ORCID: <https://orcid.org/0000-0002-2767-3243>),
  John Platig [aut],
  Marieke Kuijjer [aut] (ORCID: <https://orcid.org/0000-0001-6280-3130>),
  Megha Padi [aut] (ORCID: <https://orcid.org/0000-0002-3446-4562>),
  Rebekka Burkholz [aut],
  Des Weighill [aut] (ORCID: <https://orcid.org/0000-0003-4979-5871>),
  Chen Chen [aut] (ORCID: <https://orcid.org/0000-0002-8042-7201>),
  Kate Shutta [aut] (ORCID: <https://orcid.org/0000-0003-0402-3771>)
Maintainer: Marouen Ben Guebila <marouen.b.guebila@gmail.com>
Built: R 4.5.2; ; 2026-02-28 04:03:02 UTC; windows
