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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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: Calibration and a real dataset | HTML | R Script |
| levi: Which null answers which question | 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/levi/ |
| Package Short Url | https://bioconductor.org/packages/levi/ |
| Package Downloads Report | Download Stats |