Package: lionessR
Title: Modeling networks for individual samples using LIONESS
Version: 1.23.0
Description: LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.
Authors@R: c(person(c("Marieke", "Lydia"), "Kuijjer", 
                    role = c("aut"), 
                    email = "marieke.kuijjer@ncmm.uio.no", 
                    comment = c(ORCID = "0000-0001-6280-3130")),
             person("Ping-Han", "Hsieh",
                    role = c("cre"),
                    email = "dn070017@gmail.com",
                    comment = c(ORCID = "0000-0003-3054-1409")))
License: MIT + file LICENSE
LazyData: TRUE
Imports: stats, SummarizedExperiment, S4Vectors
Depends: R (>= 3.6.0)
Suggests: knitr, rmarkdown, igraph, reshape2, limma,
biocViews: Network, NetworkInference, GeneExpression
BugReports: https://github.com/mararie/lionessR/issues
URL: https://github.com/mararie/lionessR
Encoding: UTF-8
RoxygenNote: 6.0.1
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/lionessR
git_branch: devel
git_last_commit: f3c557f
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 23:59:01 UTC; biocbuild
Author: Marieke Lydia Kuijjer [aut] (ORCID:
    <https://orcid.org/0000-0001-6280-3130>),
  Ping-Han Hsieh [cre] (ORCID: <https://orcid.org/0000-0003-3054-1409>)
Maintainer: Ping-Han Hsieh <dn070017@gmail.com>
Built: R 4.5.0; ; 2025-06-05 13:17:50 UTC; windows
