Package: levi 1.99.0

Jose Rybarczyk Filho

levi: Landscape Expression Visualization and Network Inference

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.

Authors:Rafael Pilan [aut], Isabelle Silva [ctb], Agnes Takeda [ctb], Jose Rybarczyk Filho [ctb, cre, ths]

levi_1.99.0.tar.gz
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levi_1.99.0.tar.gz(r-4.7-arm64)levi_1.99.0.tar.gz(r-4.7-x86_64)levi_1.99.0.tar.gz(r-4.6-arm64)levi_1.99.0.tar.gz(r-4.6-x86_64)
levi_1.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
levi/json (API)

# Install 'levi' in R:
install.packages('levi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jrybarczyk/levi/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:levi-1.31.0(bioc 3.24)levi-1.30.0(bioc 3.23)

geneexpressionmicroarraysequencingrnaseqnetworkgraphandnetworkstatisticalmethodsoftwarevisualizationguigenesetenrichmentdifferentialexpressionsinglecellproteomicscpp

4.08 score 1 stars 6 scripts 378 downloads 35 exports 78 dependencies

Last updated from:ac8c924642. Checks:1 NOTE, 15 OK. Indexed: yes.

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Exports:levileviAdjustPathwaysleviBulkGraphInferenceleviDiffleviEnrichleviFromBiocleviFromDESeq2leviFromEdgeRleviFromEdgesleviFromExpressionSetleviFromLimmaleviFromSEleviFromSeuratleviFromSTRINGleviGraphClusterInferenceleviGraphGetisOrdleviGraphMoranleviGraphRewiringInferenceleviGraphSpectrumleviGraphTFCEFreedmanLaneleviGraphTFCEInferenceleviGraphTFCERewiringleviGraphWeightedTopologyleviGridleviPseudobulkleviRegionGenesleviReplicateInferenceleviSave3DleviSingleCellGraphInferenceleviSingleCellInteractionTFCEleviSingleCellRegionalInferenceleviSingleCellTFCEInferenceleviSingleCellTopologyInferenceLEVIuireadExpColumn

Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemclicodetoolscommonmarkcpp11DelayedArraydigestdplyrfarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehtmltoolshttpuvigraphIRangesisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeotelpillarpkgconfigplyrpromisesR6rappdirsRColorBrewerRcppreshape2rlangS4ArraysS4VectorsS7sassscalesSeqinfoshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrxml2xtableXVector

levi - Landscape Expression Visualization Interface
Overview | Input Files | Gene Expression Data | Biological Network | Networks with no coordinates | Viewing Modes | Graphical User Interface (GUI) | Side panel | Results | Script Mode | Basic usage | Comparing multiple conditions (batch mode) | Signal transformation (signal_mode) | Two-color palettes | 3D Interactive Visualization | Importing from Differential Expression Tools | From DESeq2 | From edgeR | From limma | Checking the adapters without the tools | Quantitative Analysis of the Landscape | Node landscape scores | Automatic peak detection | Permutation significance test | Beyond the landscape test: replication and graph TFCE | Single-Cell RNA-seq (Seurat) | Toy datasets for testing and validation | Available datasets | Bimodal dataset | signal_mode = "logfc" with log2 microarray intensities | Multi-comparison (batch mode) and leviDiff | Real datasets from Bioconductor | RNA-seq: airway (DESeq2 + STRING) | Microarray: ALL (limma + STRING) | scRNA-seq: PBMC 10x (Seurat + STRING) | Building networks from STRING | Saving and reusing a downloaded network | Layout guide | Species codes | Full pipeline example (RNA-seq + STRING) | Session Information | Signal contracts and reproducibility | References
Rendered fromlevi.Rmdusingknitr::rmarkdown

Last update: 2026-09-19
Started: 2018-10-04

levi: A Complete User Guide
Introduction | Installation | Core concepts | The landscape score | The readExpColumn() helper | Signal transformation modes | Toy datasets | Hub topology | Gradient topology | Bimodal topology — simultaneous peak and valley | Flat expression — null control | Sparse expression — missing gene handling | Node scores and peak detection | Permutation significance test | Batch mode and multi-comparison | leviGrid — side-by-side comparison | leviDiff — landscape subtraction | Differential expression adapters | leviFromDESeq2 | leviFromEdgeR | leviFromLimma | leviFromSeurat | leviFromSE — SummarizedExperiment | Running the adapters here | Building networks from STRING | Layout algorithms | Species codes | Saving and reusing networks | Real-data examples | RNA-seq: airway (DESeq2 + STRING) | Microarray: ALL leukemia (limma + STRING) | scRNA-seq: PBMC (Seurat + STRING) | Enrichment analysis — leviEnrich | 3-D interactive visualization | Interactive GUI — LEVIui | Visualization parameters | Colour palettes | Session Information | Signal contracts and reproducibility | References
Rendered fromlevi_guide.Rmdusingknitr::rmarkdown

Last update: 2026-09-19
Started: 2026-09-15

levi: Calibration and a real dataset
Why this vignette exists | Type I error under the global null | Power against effect size | How much does the layout matter? | A real dataset: dexamethasone in airway smooth muscle | The landscape and its node-label test | Replication: the sample-label tests | Is it the wiring? | Reproducing the study | Session information | References
Rendered fromlevi_validation.Rmdusingknitr::rmarkdown

Last update: 2026-09-19
Started: 2026-09-15

levi: Which null answers which question
Three nulls, three questions | Node-label null: the landscape test | The legacy cell mode | Sample-label null: biological replication | Paired designs and covariates | How small a design can be | Edge null: is it the wiring? | Autocorrelation on the graph | Running in parallel | Reporting checklist | Session information | References
Rendered fromlevi_inference.Rmdusingknitr::rmarkdown

Last update: 2026-09-19
Started: 2026-09-15

Readme and manuals

Help Manual

Help pageTopics
Bimodal toy datasetbimodal_dataset bimodal_expression bimodal_network
Flat (null-expression) toy datasetflat_dataset flat_expression flat_network
Gradient-topology toy datasetgradient_dataset gradient_expression gradient_network
Hub-topology toy datasethub_dataset hub_expression hub_network
levilevi
Adjust regional LEVI results across pathways or networksleviAdjustPathways
Bulk RNA-seq graph-cluster inferenceleviBulkGraphInference
leviDiffleviDiff
leviEnrichleviEnrich
leviFromBiocleviFromBioc
leviFromDESeq2leviFromDESeq2
leviFromEdgeRleviFromEdgeR
leviFromEdgesleviFromEdges
leviFromExpressionSetleviFromExpressionSet
leviFromLimmaleviFromLimma
leviFromSEleviFromSE
leviFromSeuratleviFromSeurat
leviFromSTRINGleviFromSTRING
Graph-connected cluster-mass inference from biological replicatesleviGraphClusterInference
Getis-Ord hotspots and coldspots on a biological graphleviGraphGetisOrd
Moran global and local autocorrelation on a biological graphleviGraphMoran
Degree-preserving rewiring test for graph clustersleviGraphRewiringInference
Laplacian smoothness and graph-Fourier low-frequency energyleviGraphSpectrum
Graph TFCE with Freedman-Lane residual permutationleviGraphTFCEFreedmanLane
Threshold-free graph-cluster enhancement with sample-label inferenceleviGraphTFCEInference
Degree-preserving rewiring sensitivity test for graph TFCEleviGraphTFCERewiring
Weighted Moran and Laplacian statistics for scored biological interactionsleviGraphWeightedTopology
leviGridleviGrid
Aggregate single-cell counts to pseudobulksleviPseudobulk
Attribute a LEVI region to nearby network genesleviRegionGenes
Regional inference from biological replicatesleviReplicateInference
Save the 3D landscape surface from a chosen viewpointleviSave3D
Single-cell pseudobulk graph-cluster inferenceleviSingleCellGraphInference
Cell-type-specific condition interaction with joint graph TFCE inferenceleviSingleCellInteractionTFCE
Joint regional inference for paired single-cell pseudobulksleviSingleCellRegionalInference
Cell-type-specific TFCE inference for pseudobulk single-cell RNA-seqleviSingleCellTFCEInference
Run Moran, Laplacian/Fourier and rewiring tests per cell typeleviSingleCellTopologyInference
LEVIui - Interactive Shiny GUI for leviLEVIui
Log2-intensity (logfc-mode) toy datasetlogfc_dataset logfc_expression logfc_network
Multi-comparison toy datasethub_multicomp_expression multicomp_dataset
Print a levi resultprint.levi_result
readExpColumn - Define expression comparisons for levireadExpColumn
Sparse-expression toy datasetsparse_dataset sparse_expression sparse_network