Package: netZooR
Type: Package
Title: A Menagerie of Methods for the Inference and Analysis of Gene
        Regulatory Networks
Version: 1.14.2
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/
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: RELEASE_3_22
git_last_commit: d0a99c4
git_last_commit_date: 2026-03-13
Repository: Bioconductor 3.22
Date/Publication: 2026-03-13
NeedsCompilation: no
Packaged: 2026-03-13 23:03:33 UTC; biocbuild
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>
