{ "_id": "6ad2643d7af56c173f1206ed", "Package": "spatialDWLS", "Title": "Cell Type Deconvolution of Spatial Transcriptomics with Dampened\nWeighted Least Squares", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Rui\", \"Dong\", role = \"aut\",\ncomment = \"original spatialDWLS method and implementation\"),\nperson(\"Guo-Cheng\", \"Yuan\", email = \"guo-cheng.yuan@mssm.edu\",\nrole = \"aut\"),\nperson(\"Ruben\", \"Dries\", email = \"rubendries@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7650-7754\")),\nperson(\"Jiaji\", \"George Chen\", email = \"jiajic@bu.edu\", role = \"ctb\",\ncomment = \"package and website\")\n)", "Description": "Estimates the cell type composition of each spot of a\nspatial transcriptomics experiment from a single-cell\nreference, following spatialDWLS (Dong and Yuan 2021,\n), which builds on dampened\nweighted least squares (DWLS; Tsoucas et al. 2019,\n). Spots are solved in two\nrounds: candidate cell types are chosen per cluster by\nenrichment, then each spot is re-solved against the types\npresent in it. Works on dense or sparse matrices, in parallel\nthrough 'BiocParallel', and over windows of spots for\nexpression stores that do not fit in memory.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://drieslab.github.io/spatialDWLS/,\nhttps://github.com/drieslab/spatialDWLS", "BugReports": "https://github.com/drieslab/spatialDWLS/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.1", "Repository": "https://drieslab.r-universe.dev", "Date/Publication": "2026-10-16 14:36:46 UTC", "RemoteUrl": "https://github.com/drieslab/spatialDWLS", "RemoteRef": "HEAD", "RemoteSha": "45d201da6af14d23ffa718858a223c731563a2d5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 17:42:34 UTC", "User": "root" }, "Author": "Rui Dong [aut] (original spatialDWLS method and implementation),\nGuo-Cheng Yuan [aut],\nRuben Dries [aut, cre] (ORCID: ),\nJiaji George Chen [ctb] (package and website)", "Maintainer": "Ruben Dries ", "_user": "drieslab", "_type": "src", "_file": "spatialDWLS_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/e39427ef7a70b13adeb6c397a6085b36b06091e17d3a94cc951431e77b40d8a6", "_filesize": 176142, "_sha256": "e39427ef7a70b13adeb6c397a6085b36b06091e17d3a94cc951431e77b40d8a6", "_expires": "2027-01-24T17:51:55.000Z", "_created": "2026-10-16T17:42:34.000Z", "_published": "2026-10-16T17:51:57.496Z", "_buildurl": "https://github.com/r-universe/drieslab/actions/runs/38941369025", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117110957156, "time": 126, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12063577609" }, { "job": 117110957131, "time": 125, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12063891388" }, { "job": 117110957375, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12063568522" }, { "job": 117110957112, "time": 129, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12064051248" }, { "job": 117109699050, "time": 175, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12062724758" }, { "job": 117110957167, "time": 99, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12063173562" }, { "job": 117110957208, "time": 91, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12063702029" }, { "job": 117110957161, "time": 90, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12063762050" }, { "job": 117110957228, "time": 94, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12063208015" } ], "_upstream": "https://github.com/drieslab/spatialDWLS", "_commit": { "id": "45d201da6af14d23ffa718858a223c731563a2d5", "author": "RubD ", "committer": "RubD ", "message": "Author order: original method authors first\n\nRui Dong and Guo-Cheng Yuan, who wrote spatialDWLS, are listed first;\nRuben Dries stays maintainer; George Chen is a contributor for the\npackage and website. The Giotto article's render script no longer\nneeds a local Giotto checkout now that Giotto 4.3.2 is merged; its\noutputs re-rendered byte-identical against the merged Giotto.\n\nCo-Authored-By: Claude Opus 5.5 \n", "time": 1792161406 }, "_maintainer": { "name": "Ruben Dries", "email": "rubendries@gmail.com", "login": "rubd", "bluesky": "@rndries.bsky.social", "twitter": "@RnDries", "description": "", "uuid": 8243389, "orcid": "0000-0001-7650-7754" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Matrix", "role": "Imports" }, { "package": "MatrixGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "quadprog", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "drieslab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-42", "n": 3 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "rubd", "count": 3, "uuid": 8243389 } ], "_userbio": { "uuid": 63752180, "type": "organization", "name": "Dries lab", "followers": 49, "description": "The Lab of Systems and Spatial Oncology" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/spatialDWLS" }, "_devurl": "https://github.com/drieslab/spatialdwls", "_pkgdown": "https://drieslab.github.io/spatialDWLS/", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/spatialDWLS.html", "LICENSE" ], "_cranurl": false, "_exports": [ "dwls", "dwls_signature", "dwls_stream" ], "_help": [ { "page": "dwls", "title": "Deconvolve spots into cell type proportions", "topics": [ "dwls" ] }, { "page": "dwls_signature", "title": "Build a DWLS signature matrix", "topics": [ "dwls_signature" ] }, { "page": "dwls_stream", "title": "Deconvolve spots read in windows", "topics": [ "dwls_stream" ] } ], "_readme": "https://github.com/drieslab/spatialDWLS/raw/HEAD/README.md", "_rundeps": [ "lattice", "Matrix", "MatrixGenerics", "matrixStats", "quadprog" ], "_vignettes": [ { "source": "spatialDWLS.Rmd", "filename": "spatialDWLS.html", "title": "Get started with spatialDWLS", "engine": "knitr::rmarkdown", "headings": [ "Simulate a small dataset with known answers", "1. 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