Package: scGraphVerse
Title: scGraphVerse: A Gene Network Analysis Package
Version: 1.3.0
Authors@R: c(
    person("Francesco", "Cecere", 
           email = "francesco.cecerengs@gmail.com", 
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0329-0870")),
    person("Annamaria", "Carissimo", 
           role = "aut"),
    person("Daniela", "De Canditiis", 
           role = "aut"),
    person("Claudia", "Angelini", 
           role = c("aut", "fnd")))
Description: A package for inferring, comparing, and visualizing gene
        networks from single-cell RNA sequencing data. It integrates
        multiple methods (GENIE3, GRNBoost2, ZILGM, PCzinb, and JRF)
        for robust network inference, supports consensus building
        across methods or datasets, and provides tools for evaluating
        regulatory structure and community similarity. GRNBoost2
        requires Python package 'arboreto' which can be installed using
        init_py(install_missing = TRUE). This package includes adapted
        functions from ZILGM (Park et al., 2021), JRF (Petralia et al.,
        2015), and learn2count (Nguyen et al. 2023) packages with
        proper attribution under GPL-2 license.
License: GPL-3 + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews: GeneRegulation, NetworkInference, SingleCell, RNASeq,
        Visualization, Software, GraphAndNetwork, GeneSetEnrichment,
        NetworkEnrichment, Pathways, Sequencing, Reactome, Network,
        KEGG
URL: https://ngsFC.github.io/scGraphVerse
BugReports: https://github.com/ngsFC/scGraphVerse/issues
Depends: R (>= 4.5.0)
Imports: BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG,
        GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment,
        SummarizedExperiment, distributions3, dplyr, grDevices,
        graphics, httr, igraph, jsonlite, methods, parallel,
        reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors,
        graph, mpath
Suggests: AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot,
        fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db,
        org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA,
        rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0),
        knitr, rmarkdown, tidyverse, magick, celldex, SingleR,
        TENxPBMCData, scater, GenomeInfoDb, GenomicRanges,
VignetteBuilder: knitr
LazyData: false
SystemRequirements: Python (>= 3.6) and arboreto Python package for
        GRNBoost2 method. Use init_py(install_missing = TRUE) for
        automated installation.
Config/pak/sysreqs: libglpk-dev libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:05:44 UTC
RemoteUrl: https://github.com/bioc/scGraphVerse
RemoteRef: HEAD
RemoteSha: 9153b373555a0c4b952eaed4ca587cb6d952f867
NeedsCompilation: yes
Packaged: 2026-07-18 09:09:47 UTC; root
Author: Francesco Cecere [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0329-0870>),
  Annamaria Carissimo [aut],
  Daniela De Canditiis [aut],
  Claudia Angelini [aut, fnd]
Maintainer: Francesco Cecere <francesco.cecerengs@gmail.com>