Package: levi
Type: Package
Title: Landscape Expression Visualization and Network Inference
Version: 1.99.0
Authors@R: 
    c(person(given = "Rafael",
                 family = "Pilan",
                 role = "aut",
                 email = "rafael.pilan@unesp.br"),
      person(given = "Isabelle",
                 family = "Silva",
                 role = "ctb"),
      person(given = "Agnes",
                family = "Takeda",
                role = "ctb"),
      person(given = "Jose",
                family = "Rybarczyk Filho",
                role = c("ctb", "cre", "ths"),
                email = "jose.luiz@unesp.br",
                comment = c(ORCID = "0000-0002-0757-3608"))
			 )
Description: Projects gene expression onto the plane of a biological
        network and draws it as a landscape: a Gaussian-kernel weighted
        surface on an absolute scale where 0.5 means no change. Regions
        of the landscape are tested by permutation, either conditional
        on the network and layout (node-label shuffling, maximum
        regional mass) or against biological replication (sample-label
        permutation, with blocking). Graph-native tests complement the
        landscape: threshold-free cluster enhancement on network
        components, Moran and Getis-Ord autocorrelation, Laplacian
        smoothness, Freedman-Lane residual permutation with covariates
        and degree-preserving rewiring nulls. Pseudobulk workflows for
        single-cell RNA-seq permute donors rather than cells. Adapters
        read DESeq2, edgeR, limma and Seurat results,
        SummarizedExperiment objects and STRING networks. A Shiny
        interface covers the interactive visualization.
URL: https://bioconductor.org/packages/levi
BugReports: https://github.com/jrybarczyk/levi/issues
Encoding: UTF-8
Imports: BiocParallel, Matrix, dplyr (>= 0.7.4), ggplot2 (>= 2.2.1),
        grid, grDevices, igraph (>= 1.2.1), methods, Rcpp (>= 0.12.18),
        reshape2 (>= 1.4.3), shiny (>= 1.0.5), stats,
        SummarizedExperiment, utils, withr, xml2 (>= 1.2.0)
Suggests: testthat, BiocStyle, knitr, rmarkdown, DT (>= 0.4),
        shinydashboard (>= 0.7.0), shinyjs (>= 1.0), plotly (>= 4.9.0),
        ggrepel, patchwork, cowplot, gridExtra, htmlwidgets, magick,
        reticulate, Biobase, DESeq2, edgeR, limma, Seurat,
        SingleCellExperiment, S4Vectors, clusterProfiler, org.Hs.eg.db,
        STRINGdb
LinkingTo: Rcpp
License: GPL (>= 2)
biocViews: GeneExpression, Microarray, Sequencing, RNASeq, Network,
        GraphAndNetwork, StatisticalMethod, Software, Visualization,
        GUI, GeneSetEnrichment, DifferentialExpression, SingleCell,
        Proteomics
VignetteBuilder: knitr
LazyLoad: yes
NeedsCompilation: yes
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-19 22:48:21 UTC
RemoteUrl: https://github.com/bioc/levi
RemoteRef: HEAD
RemoteSha: ac8c924642aac186de9e2ca9ccc0b8652fd5ab5c
Packaged: 2026-09-20 06:35:17 UTC; root
Author: Rafael Pilan [aut],
  Isabelle Silva [ctb],
  Agnes Takeda [ctb],
  Jose Rybarczyk Filho [ctb, cre, ths] (ORCID:
    <https://orcid.org/0000-0002-0757-3608>)
Maintainer: Jose Rybarczyk Filho <jose.luiz@unesp.br>