Package: hcocena
Title: Horizontal Integration and Analysis of Multiple Transcriptomics
        Datasets
Version: 0.99.12
Authors@R: c(
    person(given = "Thomas",
           family = "Ulas",
           role = c("aut", "cre"),
           email = "t.ulas@uni-bonn.de",
           comment = c(ORCID = "0000-0002-9785-4197")),
    person(given = "Waqar",
           family = "Hanif",
           role = c("ctb")))
Description: Tools for the joint analysis of multiple transcriptomics
        datasets using a network-based integration approach. The
        package provides an S4 object model based on
        MultiAssayExperiment for reproducible analysis of single-layer
        and multi-layer studies. It includes workflows for clustering,
        module visualization, functional annotation, upstream
        inference, and longitudinal follow-up while retaining
        compatibility helpers for legacy hCoCena objects.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.5.0)
biocViews: Software, Clustering, GeneExpression, KEGG, Network,
        NetworkInference, Transcriptomics, WorkflowStep
BiocType: Software
URL: https://github.com/BioCompNet/hcocena
BugReports: https://github.com/BioCompNet/hcocena/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: Cairo (>= 1.5-12.2), circlize, clusterProfiler (>= 3.18.1),
        ComplexHeatmap (>= 2.6.2), cowplot (>= 1.1.1), dendextend (>=
        1.15.1), dplyr (>= 1.0.6), factoextra (>= 1.0.7), ggplot2 (>=
        3.3.5), ggsci (>= 2.9), graphics (>= 4.0.3), grDevices (>=
        4.0.3), grid (>= 4.0.3), gtools (>= 3.9.2), Hmisc (>= 4.5-0),
        httr (>= 1.4.2), igraph (>= 1.2.6), jsonlite (>= 1.7.2),
        leidenAlg (>= 0.1.1), leidenbase (>= 0.1.25), magrittr (>=
        2.0.1), Matrix, methods, MultiAssayExperiment, openxlsx (>=
        4.2.4), patchwork (>= 1.1.3), pheatmap (>= 1.0.12), plotly (>=
        4.9.4.1), purrr (>= 0.3.4), RColorBrewer (>= 1.1-2), readr (>=
        2.0.1), reshape2, rlist (>= 0.4.6.1), S4Vectors, scales (>=
        1.1.1), stringi (>= 1.6.2), stringr (>= 1.5.1),
        SummarizedExperiment, tibble (>= 3.1.2), tidyselect (>= 1.1.1),
        zip (>= 2.3.0)
Suggests: BiocStyle, CALIBERrfimpute, clipr, decoupleR, dorothea,
        ellmer, emmeans, ggh4x, ggrepel, graphlayouts, GSVA,
        htmlwidgets, knitr (>= 1.33), lme4, limma, mice, networkD3 (>=
        0.4), nlme, OmnipathR, png, progeny, RANN, RCy3 (>= 2.10.2),
        RcppAnnoy, repr, rmarkdown, SingleCellExperiment, testthat (>=
        3.0.0), umap, uwot, withr
VignetteBuilder: knitr
Config/testthat/edition: 3
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 perl libx11-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-03 21:41:46 UTC
RemoteUrl: https://github.com/BiocStaging/hcocena
RemoteRef: HEAD
RemoteSha: d0b918c0e0b390678cceba94ccaa9d2fc0ddd95d
Packaged: 2026-10-04 00:56:37 UTC; root
Author: Thomas Ulas [aut, cre] (ORCID: <https://orcid.org/0000-0002-9785-4197>),
  Waqar Hanif [ctb]
Maintainer: Thomas Ulas <t.ulas@uni-bonn.de>