levi
This is the development version of levi; for the stable release version, see levi.
Landscape Expression Visualization and Network Inference
Bioconductor version: Development (3.24)
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.
Author: Rafael Pilan [aut], Isabelle Silva [ctb], Agnes Takeda [ctb], Jose Rybarczyk Filho [ctb, cre, ths] 
Maintainer: Jose Rybarczyk Filho <jose.luiz at unesp.br>
citation("levi")):Rafael Pilan. levi: Landscape Expression Visualization and Network Inference. doi:10.18129/B9.bioc.levi, R package version 1.99.0, https://bioconductor.org/packages/levi.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("levi")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("levi")| levi: A Complete User Guide | HTML | R Script |
| levi: Which null answers which question | HTML | R Script |
| levi: Calibration and a real dataset | HTML | R Script |
| "Using levi" | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, Proteomics, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Visualization |
| Version | 1.99.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL (>= 2) |
| Depends | |
| 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) |
| System Requirements | |
| URL | https://bioconductor.org/packages/levi |
| Bug Reports | https://github.com/jrybarczyk/levi/issues |
See More
| 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 |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | levi_1.99.0.tar.gz |
| Windows Binary (x86_64) | levi_1.99.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | levi_1.99.0.tgz |
| macOS Binary (sonoma-arm64) | levi_1.99.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/levi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/levi |
| Package Short Url | https://bioconductor.org/packages/levi/ |
| Package Downloads Report | Download Stats |