{ "_id": "6a1afa821d7bb097a09fc0c7", "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": "2026-05-30 09:48:52 UTC", "User": "root" }, "Author": "Marc Elosua-Bayes [aut, cre],\nZachary DeBruine [aut],\nHelena L. Crowell [aut]", "Maintainer": "Marc Elosua-Bayes ", "MD5sum": "0228660a475bd4369c74308d22b93885", "_user": "bioc", "_type": "src", "_file": "SPOTlight_1.17.0.tar.gz", "_fileid": "08111e25dd52bce0194d9bb0b0acff6f7e137ff56d63f3b5de7472d3ff9a67c5", "_filesize": 4223032, "_sha256": "08111e25dd52bce0194d9bb0b0acff6f7e137ff56d63f3b5de7472d3ff9a67c5", "_created": "2026-05-30T09:48:52.000Z", "_published": "2026-05-30T14:56:02.651Z", "_jobs": [ { "job": 78640730158, "time": 258, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307530179" }, { "job": 78640730302, "time": 532, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7307355013" }, { "job": 78640730212, "time": 435, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307549016" }, { "job": 78640730207, "time": 360, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307338739" }, { "job": 78640730210, "time": 457, "config": 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unique features mgs <- lapply(ks, function(k) g1 <- mgs[[k]][[gene_id]] g2 <- unlist(lapply(mgs[ks != 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": "plotSpatialScatterpie", "title": "Spatial scatterpie", "topics": [ "plotSpatialScatterpie" ] }, { "page": "plotTopicProfiles", "title": "Plot NMF topic profiles", "topics": [ "plotTopicProfiles" ] }, { "page": "runDeconvolution", "title": "Run Deconvolution using NNLS model", "topics": [ "runDeconvolution" ] }, { "page": "SPOTlight", "title": "Deconvolution of mixture using single-cell data", "topics": [ "SPOTlight" ] }, { "page": "trainNMF", "title": "train NMF model", "topics": [ "trainNMF" ] } ], "_readme": "https://github.com/bioc/SPOTlight/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "S4Arrays", "S4Vectors", "S7", 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