Package: netZooR
Type: Package
Title: A menagerie of methods for the inference and analysis of gene
        regulatory networks
Version: 1.17.0
Date: 2025-07-31
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: netZooR 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 mutliple
        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 expresssion data for tissue-specific analyses and SAMBAR
        infers missing mutation data based on pathway information.
Depends: R (>= 4.2.0), igraph, reticulate, pandaR, Biobase,
Remotes: stan-dev/cmdstanr, jnpaulson/pandaR, cytoscape/RCy3
biocViews: GeneExpression, GeneRegulation, GraphAndNetwork, Microarray,
        Network, NetworkInference, Transcription
Imports: cmdstanr, AnnotationDbi, assertthat, biomaRt, cmdstanr,
        corpcor, data.table, doParallel, downloader, dplyr, edgeR,
        foreach, GeneNet, ggdendro, ggplot2, GO.db, GOstats, gplots,
        graphics, grid, limma, loo, MASS, Matrix, matrixcalc,
        matrixStats, matrixTests, methods, nnet, org.Hs.eg.db,
        parallel, penalized, preprocessCore, quantro, rARPACK,
        RColorBrewer, RCy3, readr, reshape, reshape2, stats, STRINGdb,
        tidyr, utils, vegan, viridisLite,
License: GPL-3
Encoding: UTF-8
LazyData: false
Suggests: dorothea, knitr, pkgdown, rmarkdown, testthat (>= 2.1.0),
Additional_repositories: https://stan-dev.r-universe.dev
VignetteEngine: knitr
VignetteBuilder: knitr
RoxygenNote: 7.3.2
BugReports: https://github.com/netZoo/netZooR/issues
URL: https://github.com/netZoo/netZooR, https://netzoo.github.io/
PackageStatus: Deprecated
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        python3 libx11-dev xz-utils libzmq3-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:30 UTC
RemoteUrl: https://github.com/bioc/netZooR
RemoteRef: HEAD
RemoteSha: ad27b19fcdded0383d464ae8fa8c00c0c94c402a
NeedsCompilation: no
Packaged: 2026-10-06 11:35:40 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>