{ "_id": "6aaf82cc3d719c1f8407e34f", "Package": "levi", "Type": "Package", "Title": "Landscape Expression Visualization and Network Inference", "Version": "1.99.0", "Authors@R": "c(person(given = \"Rafael\",\nfamily = \"Pilan\",\nrole = \"aut\",\nemail = \"rafael.pilan@unesp.br\"),\nperson(given = \"Isabelle\",\nfamily = \"Silva\",\nrole = \"ctb\"),\nperson(given = \"Agnes\",\nfamily = \"Takeda\",\nrole = \"ctb\"),\nperson(given = \"Jose\",\nfamily = \"Rybarczyk Filho\",\nrole = c(\"ctb\", \"cre\", \"ths\"),\nemail = \"jose.luiz@unesp.br\",\ncomment = c(ORCID = \"0000-0002-0757-3608\"))\n)", "Description": "Projects gene expression onto the plane of a biological\nnetwork and draws it as a landscape: a Gaussian-kernel weighted\nsurface on an absolute scale where 0.5 means no change. Regions\nof the landscape are tested by permutation, either conditional\non the network and layout (node-label shuffling, maximum\nregional mass) or against biological replication (sample-label\npermutation, with blocking). Graph-native tests complement the\nlandscape: threshold-free cluster enhancement on network\ncomponents, Moran and Getis-Ord autocorrelation, Laplacian\nsmoothness, Freedman-Lane residual permutation with covariates\nand degree-preserving rewiring nulls. Pseudobulk workflows for\nsingle-cell RNA-seq permute donors rather than cells. Adapters\nread DESeq2, edgeR, limma and Seurat results,\nSummarizedExperiment objects and STRING networks. A Shiny\ninterface covers the interactive visualization.", "URL": "https://bioconductor.org/packages/levi", "BugReports": "https://github.com/jrybarczyk/levi/issues", "Encoding": "UTF-8", "License": "GPL (>= 2)", "biocViews": "GeneExpression, Microarray, Sequencing, RNASeq, Network,\nGraphAndNetwork, StatisticalMethod, Software, Visualization,\nGUI, GeneSetEnrichment, DifferentialExpression, SingleCell,\nProteomics", "VignetteBuilder": "knitr", "LazyLoad": "yes", "NeedsCompilation": "yes", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-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": { "Date": "2026-09-20 06:35:17 UTC", "User": "root" }, "Author": "Rafael Pilan [aut],\nIsabelle Silva [ctb],\nAgnes Takeda [ctb],\nJose Rybarczyk Filho [ctb, cre, ths] (ORCID:\n)", "Maintainer": "Jose Rybarczyk Filho ", "_user": "bioc", "_type": "src", "_file": "levi_1.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/aadbf7c934adc70154c2eb4921c8fc458d57342056cf9b281d5eca2ca1dd9f3e", "_filesize": 5928814, "_sha256": "aadbf7c934adc70154c2eb4921c8fc458d57342056cf9b281d5eca2ca1dd9f3e", "_expires": "2026-12-29T06:52:57.000Z", "_created": "2026-09-20T06:35:17.000Z", "_published": "2026-09-20T06:53:00.010Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35494372010", "_status": "success", "_upstream": "https://github.com/bioc/levi", "_commit": { "id": "ac8c924642aac186de9e2ca9ccc0b8652fd5ab5c", "author": "jrybarczyk ", "committer": "jrybarczyk ", "message": "Build the TFCE graph once per call instead of at every threshold\n\n.componentsAt() rebuilt the igraph object for each of the 100 integration\nsteps, on both sides, in every permutation draw. The graph is now built\nonce in .tfce() and the components are recomputed only when the active\nset changes between consecutive thresholds. Results are identical; the\nleviSingleCellTFCEInference() example drops from 5.2 s to 0.4 s, under the\n5 s limit of the Bioconductor build report.\n\nCo-Authored-By: Claude Fable 5.1 \n", "time": 1789858101 }, "_maintainer": { "name": "Jose Rybarczyk Filho", "email": "jose.luiz@unesp.br", "login": "jrybarczyk", "description": "", "uuid": 13757354, "orcid": "0000-0002-0757-3608" }, "_distro": "resolute", "_jobs": [ { "job": 106035365806, "time": 262, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "10599598861" }, { "job": 106035365797, "time": 415, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10599958607" }, { "job": 106035365810, "time": 555, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10599669043" }, { "job": 106035365846, "time": 384, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10599549042" }, { "job": 106035365776, "time": 481, "config": "linux-release-x86_64", "r": 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