{ "_id": "6a1af98e1d7bb097a09fb782", "Package": "SCnorm", "Title": "Normalization of single cell RNA-seq data", "Version": "1.35.0", "Author": "Rhonda Bacher", "Maintainer": "Rhonda Bacher ", "Description": "This package implements SCnorm — a method to normalize\nsingle-cell RNA-seq data.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "biocViews": "Normalization, RNASeq, SingleCell, ImmunoOncology", "URL": "https://github.com/rhondabacher/SCnorm", "BugReports": "https://github.com/rhondabacher/SCnorm/issues", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:04 UTC", "RemoteUrl": "https://github.com/bioc/SCnorm", "RemoteRef": "HEAD", "RemoteSha": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:48:56 UTC", "User": "root" }, "MD5sum": "c3716630fefa4d9bff3ba5211f9dd289", "_user": "bioc", "_type": "src", "_file": "SCnorm_1.35.0.tar.gz", "_fileid": "7fd75d1a74a508637be956c7053c92c7fee28e10f3ee00c71da30dd6d4011fbc", "_filesize": 3250019, "_sha256": "7fd75d1a74a508637be956c7053c92c7fee28e10f3ee00c71da30dd6d4011fbc", "_created": "2026-05-30T09:48:56.000Z", "_published": "2026-05-30T14:51:58.002Z", "_jobs": [ { "job": 78640726163, "time": 192, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307522149" }, { "job": 78640726168, "time": 316, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307532784" }, { "job": 78640726170, "time": 356, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307536357" }, { "job": 78640726162, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309016041" }, { "job": 78640726165, "time": 166, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309017452" }, { "job": 78639922347, "time": 362, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307302978" }, { "job": 78640726178, "time": 151, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307517768" }, { "job": 78640726174, "time": 239, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307524711" }, { "job": 78640726184, "time": 268, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307527115" }, { "job": 78640726177, "time": 230, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307523607" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SCnorm", "_commit": { "id": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380364 }, "_maintainer": { "name": "Rhonda Bacher", "email": "rbacher@ufl.edu", "login": "rhondabacher", "twitter": "@rbacher", "description": "Associate Professor of Biostatistics at the University of Florida", "uuid": 6611436 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "quantreg", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "moments", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "forcats", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-24", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "normalization", "rnaseq", "singlecell", "immunooncology" ], "_stars": 51, "_contributors": [ { "user": "rhondabacher", "count": 113, "uuid": 6611436 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "link-ny", "count": 2, "uuid": 4392950 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "jenzopr", "count": 2, "uuid": 8362850 }, { "user": "alaindomissy", "count": 1, "uuid": 71084 }, { "user": "golharam", "count": 1, "uuid": 671079 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 488, "source": "https://www.bioconductor.org/packages/stats/bioc/SCnorm" }, "_mentions": 15, "_devurl": "https://github.com/rhondabacher/scnorm", "_searchresults": 81, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SCnorm.html", "manual.pdf" ], "_homeurl": "https://github.com/rhondabacher/scnorm", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getCounts", "getSlopes", "plotCountDepth", "plotWithinFactor", "results", "scaleNormMultCont", "SCnorm" ], "_datasets": [ { "name": "ExampleSimSCData", "title": "Example datasets for SCnorm", "object": "ExampleSimSCData", "class": [ "matrix", "array" ], "fields": [ "Cell_1", "Cell_2", "Cell_3", "Cell_4", "Cell_5", "Cell_6", "Cell_7", "Cell_8", "Cell_9", "Cell_10", "Cell_11", "Cell_12", "Cell_13", "Cell_14", "Cell_15", "Cell_16", "Cell_17", "Cell_18", "Cell_19", "Cell_20", "Cell_21", "Cell_22", "Cell_23", "Cell_24", "Cell_25", "Cell_26", "Cell_27", "Cell_28", "Cell_29", "Cell_30", "Cell_31", "Cell_32", "Cell_33", "Cell_34", "Cell_35", "Cell_36", "Cell_37", "Cell_38", "Cell_39", "Cell_40", "Cell_41", "Cell_42", "Cell_43", "Cell_44", "Cell_45", "Cell_46", "Cell_47", "Cell_48", "Cell_49", "Cell_50", "Cell_51", "Cell_52", "Cell_53", "Cell_54", "Cell_55", "Cell_56", "Cell_57", "Cell_58", "Cell_59", "Cell_60", "Cell_61", "Cell_62", "Cell_63", "Cell_64", "Cell_65", "Cell_66", "Cell_67", "Cell_68", "Cell_69", "Cell_70", "Cell_71", "Cell_72", "Cell_73", "Cell_74", "Cell_75", "Cell_76", "Cell_77", "Cell_78", "Cell_79", "Cell_80", "Cell_81", "Cell_82", "Cell_83", "Cell_84", "Cell_85", "Cell_86", "Cell_87", "Cell_88", "Cell_89", "Cell_90" ], "rows": 5000, "table": true, "tojson": true } ], "_help": [ { "page": "correctWithin", "title": "correctWithin", "topics": [ "correctWithin" ] }, { "page": "evaluateK", "title": "Evaluate normalization using K slope groups", "topics": [ "evaluateK" ] }, { "page": "ExampleSimSCData", "title": "Example datasets for SCnorm", "topics": [ "ExampleSimSCData" ] }, { "page": "generateEvalPlot", "title": "Internal plotting function.", "topics": [ "generateEvalPlot" ] }, { "page": "getCounts", "title": "getCounts", "topics": [ "getCounts" ] }, { "page": "getDens", "title": "getDens", "topics": [ "getDens" ] }, { "page": "getSlopes", "title": "Estimate gene specific count-depth relationships", "topics": [ "getSlopes" ] }, { "page": "GetTD", "title": "Fit group regression for specific quantile and degree", "topics": [ "GetTD" ] }, { "page": "normWrapper", "title": "Iteratively fit group regression and evaluate to choose optimal K", "topics": [ "normWrapper" ] }, { "page": "plotCountDepth", "title": "Evaluate the count-depth relationship before (or after) normalizing the data.", "topics": [ "plotCountDepth" ] }, { "page": "plotWithinFactor", "title": "Evaluate gene-specific factors in the the data.", "topics": [ "plotWithinFactor" ] }, { "page": "quickReg", "title": "quickReg", "topics": [ "quickReg" ] }, { "page": "redoBox", "title": "redoBox", "topics": [ "redoBox" ] }, { "page": "results", "title": "results", "topics": [ "results" ] }, { "page": "scaleNormMultCont", "title": "Scale multiple conditions", "topics": [ "scaleNormMultCont" ] }, { "page": "SCnorm", "title": "SCnorm", "topics": [ "SCnorm" ] }, { "page": "SCnormFit", "title": "Fit group quantile regression for K groups", "topics": [ "SCnormFit" ] }, { "page": "splitGroups", "title": "splitGroups", "topics": [ "splitGroups" ] } ], "_readme": "https://github.com/bioc/SCnorm/raw/HEAD/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "cli", "cluster", "codetools", "cpp11", "data.table", "DelayedArray", "farver", "forcats", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "moments", "pillar", "pkgconfig", "quantreg", "R6", "RColorBrewer", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SingleCellExperiment", "snow", "SparseArray", "SparseM", "SummarizedExperiment", "survival", "tibble", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "SCnorm.Rnw", "filename": "SCnorm.pdf", "title": "SCnorm Vignette", "engine": "knitr::knitr", "headings": [], "created": "2016-11-12 18:51:09", "modified": "2025-06-11 17:42:11", "commits": 27 } ], "_score": 8.69523644102421, "_indexed": true, "_nocasepkg": "scnorm", "_universes": [ "bioc", "rhondabacher" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-05-30T10:29:46.000Z", "distro": "noble", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "d610ce067b648b574fd24c0fab9ead810d4542f52ef6d14a56d247697a258b91", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.6.0", "os": "linux", "version": "1.35.0", "date": "2026-05-30T10:30:17.000Z", "distro": "noble", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "3d6a53d5300a9c2b9a8f02b29d931e02aace71bda7e72cc8b4b1d5fb1921c6ea", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-05-30T14:50:05.000Z", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "55ef2a26f83ff8ebc47e0d32d4e8590aaa37061fba7578d3c2ea1b2a424c9754", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.6.0", "os": "mac", "version": "1.35.0", "date": "2026-05-30T14:50:05.000Z", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "0eeba765d8bf2ebb1de7cc7e1c947b8d591a75d5b4cec32111b85acc5d951d55", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-05-30T10:29:03.000Z", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "63efe33e048aa6de567cb75e7cb01339062aecd5dc14b36626cf60215ff2a4ab", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-05-30T10:28:01.000Z", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "8a5c46be97fab2040af607734970f7e4e87b81adfcccb67f9a79ba65896449c3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-05-30T10:28:20.000Z", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "910301fb32e6fb586c0a62e27ac22bf7e9edbff4fed63394141cc3479584784c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" }, { "r": "4.6.0", "os": "win", "version": "1.35.0", "date": "2026-05-30T10:27:44.000Z", "commit": "3ceb26a3ad7090785d5f226e38f850b60e5e8828", "fileid": "b9773abb82b0cba64b7ca44ed8184f88563ce7f0ba36cc4d45fec7be498157a7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676951134" } ] }