{ "_id": "6a494c30f6c47c44194994ba", "Package": "SPOTlight", "Version": "1.17.0", "Type": "Package", "Title": "`SPOTlight`: Spatial Transcriptomics Deconvolution", "Description": "`SPOTlight` provides a method to deconvolute spatial\ntranscriptomics spots using a seeded NMF approach along with\nvisualization tools to assess the results. Spatially resolved\ngene expression profiles are key to understand tissue\norganization and function. However, novel spatial\ntranscriptomics (ST) profiling techniques lack single-cell\nresolution and require a combination with single-cell RNA\nsequencing (scRNA-seq) information to deconvolute the spatially\nindexed datasets. Leveraging the strengths of both data types,\nwe developed SPOTlight, a computational tool that enables the\nintegration of ST with scRNA-seq data to infer the location of\ncell types and states within a complex tissue. SPOTlight is\ncentered around a seeded non-negative matrix factorization\n(NMF) regression, initialized using cell-type marker genes and\nnon-negative least squares (NNLS) to subsequently deconvolute\nST capture locations (spots).", "Authors@R": "c(\nperson(\"Marc\", \"Elosua-Bayes\", email=\"elosua.marc@gmail.com\", role=c(\"aut\", \"cre\")),\nperson(\"Zachary\", \"DeBruine\", email=\"zacharydebruine@gmail.com\", role=\"aut\"),\nperson(\"Helena L.\", \"Crowell\", email=\"helena@crowell.eu\", role=\"aut\"))", "biocViews": "SingleCell, Spatial, StatisticalMethod", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/MarcElosua/SPOTlight", "BugReports": "https://github.com/MarcElosua/SPOTlight/issues", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:11 UTC", "RemoteUrl": "https://github.com/bioc/SPOTlight", "RemoteRef": "HEAD", "RemoteSha": "ad59a485ef80aea3679fb1839aa622723b016ec4", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-03 19:17:46 UTC", "User": "root" }, "Author": "Marc Elosua-Bayes [aut, cre],\nZachary DeBruine [aut],\nHelena L. Crowell [aut]", "Maintainer": "Marc Elosua-Bayes ", "_user": "bioc", "_type": "src", "_file": "SPOTlight_1.17.0.tar.gz", "_fileid": "https://r2.ropensci.org/84e36a1accb27a733a923a2098ccffaddbf6c8c6f9c93ec2a3be9f873242edd7", "_filesize": 4247405, "_sha256": "84e36a1accb27a733a923a2098ccffaddbf6c8c6f9c93ec2a3be9f873242edd7", "_expires": "2026-10-12T18:08:46.000Z", "_created": "2026-07-03T19:17:46.000Z", "_published": "2026-07-04T18:08:48.527Z", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28679179601", "_status": "success", "_upstream": "https://github.com/bioc/SPOTlight", "_commit": { "id": "ad59a485ef80aea3679fb1839aa622723b016ec4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381091 }, "_maintainer": { "name": "Marc Elosua-Bayes", "email": "elosua.marc@gmail.com", "login": "marcelosua", 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k], `[[`, gene_id)) mgs[[k]][!g1 ) # W is of dimension (#groups)x(#features) with W(i,j) # equal to weight if j is marker for i, and ~0 otherwise W <- vapply(ks, function(k) w <- numeric(ng) + 1e-12 names(w) <- rownames(x) ws <- mgs[[k]][[weight_id]] w[mgs[[k]][[gene_id]]] <- ws return(w) , numeric(ng)) # there is no need to initialize H tp <- paste0(\"topic_\", seq_len(length(ks))) dimnames(W) <- list(rownames(x), tp) return(W) Filter features from expression matrix", "topics": [ ".filter" ] }, { "page": "data", "title": "Synthetic single-cell, mixture and marker data", "topics": [ "data", "getMGS", "mockSC", "mockSP" ] }, { "page": "plotCorrelationMatrix", "title": "Plot Correlation Matrix", "topics": [ "plotCorrelationMatrix" ] }, { "page": "plotImage", "title": "Plot JP(E)G/PNG/Raster/RGB images", "topics": [ "plotImage" ] }, { "page": "plotInteractions", "title": "Plot group interactions", "topics": [ "plotHeatmap", "plotInteractions", "plotNetwork" ] }, { "page": 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