{ "_id": "6a1af7881d7bb097a09fa635", "Package": "SpotClean", "Version": "1.15.0", "Date": "2024/06/08", "Title": "SpotClean adjusts for spot swapping in spatial transcriptomics\ndata", "Authors@R": "c(\nperson(\"Zijian\", \"Ni\", email=\"zni25@wisc.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1181-8337\")),\nperson(\"Christina\", \"Kendziorski\", role = \"ctb\")\n)", "biocViews": "DataImport, RNASeq, Sequencing, GeneExpression, Spatial,\nSingleCell, Transcriptomics, Preprocessing", "Description": "SpotClean is a computational method to adjust for spot\nswapping in spatial transcriptomics data. Recent spatial\ntranscriptomics experiments utilize slides containing thousands\nof spots with spot-specific barcodes that bind mRNA. Ideally,\nunique molecular identifiers at a spot measure spot-specific\nexpression, but this is often not the case due to bleed from\nnearby spots, an artifact we refer to as spot swapping.\nSpotClean is able to estimate the contamination rate in\nobserved data and decontaminate the spot swapping effect, thus\nincrease the sensitivity and precision of downstream analyses.", "License": "GPL-3", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "URL": "https://github.com/zijianni/SpotClean", "BugReports": "https://github.com/zijianni/SpotClean/issues", "Language": "en-US", "Config/pak/sysreqs": "cmake libglpk-dev make libmagick++-dev gsfonts\nlibicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev\nlibxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:28 UTC", "RemoteUrl": "https://github.com/bioc/SpotClean", "RemoteRef": "HEAD", "RemoteSha": "e4d13d631fa958185b5539ee6c588e61d75fe848", "Packaged": { "Date": "2026-05-30 09:47:03 UTC", "User": "root" }, "Author": "Zijian Ni [aut, cre] (ORCID: ),\nChristina Kendziorski [ctb]", "Maintainer": "Zijian Ni ", "MD5sum": "14a896569dd84d91fd7aa0417a46dc6c", "_user": "bioc", "_type": "src", "_file": "SpotClean_1.15.0.tar.gz", "_fileid": "0e9ce44bfcc463a40e421015eccdf143b3907539bba98e70b28775aeff02ee20", "_filesize": 4109174, "_sha256": "0e9ce44bfcc463a40e421015eccdf143b3907539bba98e70b28775aeff02ee20", "_created": "2026-05-30T09:47:03.000Z", "_published": "2026-05-30T14:43:20.310Z", "_jobs": [ { "job": 78640639727, "time": 238, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307497071" }, { "job": 78640639735, "time": 494, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307518437" }, { "job": 78640639740, "time": 552, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307523565" }, { "job": 78640639739, "time": 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