levi

Landscape Expression Visualization and Network Inference

Bioconductor version: 3.24 · Package version: 1.99.0

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("levi")