{ "_id": "6a1538ebacfb0bcc41d50163", "Package": "spqn", "Title": "Spatial quantile normalization", "Version": "1.25.0", "Description": "The spqn package implements spatial quantile normalization\n(SpQN). This method was developed to remove a mean-correlation\nrelationship in correlation matrices built from gene expression\ndata. It can serve as pre-processing step prior to a\nco-expression analysis.", "Authors@R": "c(person(\"Yi\", \"Wang\", role = c(\"cre\", \"aut\"), email = \"yiwangthu5@gmail.com\"),\nperson(c(\"Kasper\", \"Daniel\"), \"Hansen\", role = \"aut\"))", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "URL": "https://github.com/hansenlab/spqn", "BugReports": "https://github.com/hansenlab/spqn/issues", "biocViews": "NetworkInference, GraphAndNetwork, Normalization", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:29 UTC", "RemoteUrl": "https://github.com/bioc/spqn", "RemoteRef": "HEAD", "RemoteSha": "fb7533c4850a9714fa830599a5dd38474d8954aa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 06:02:30 UTC", "User": "root" }, "Author": "Yi Wang [cre, aut],\nKasper Daniel Hansen [aut]", "Maintainer": "Yi Wang ", "MD5sum": "49b22f7c1bee27d4654a382d15a178d8", "_user": "bioc", "_type": "src", "_file": "spqn_1.25.0.tar.gz", "_fileid": "d2b89cfa9a8840389f83e0393a814fde798da2fa9871eaa4b6ca9624e9c907a9", "_filesize": 2791647, "_sha256": "d2b89cfa9a8840389f83e0393a814fde798da2fa9871eaa4b6ca9624e9c907a9", "_created": "2026-05-26T06:02:30.000Z", "_published": "2026-05-26T06:08:42.979Z", "_jobs": [ { "job": 77816634357, "time": 186, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7209998565" }, { "job": 77816634305, "time": 288, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7210020377" }, { "job": 77816634258, "time": 322, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7210027609" }, { "job": 77816634274, "time": 169, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7209994939" }, { "job": 77816634272, "time": 180, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7209997177" }, { "job": 77816140156, "time": 260, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7209958144" }, { "job": 77816634296, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7209986014" }, { "job": 77816634291, "time": 242, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7210010445" }, { "job": 77816634273, "time": 259, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7210013953" }, { "job": 77816634265, "time": 222, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7210006360" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/spqn", "_commit": { "id": "fb7533c4850a9714fa830599a5dd38474d8954aa", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380749 }, "_maintainer": { "name": "Yi Wang", "email": "yiwangthu5@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "ggridges", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tools", "role": "Suggests" }, { "package": "spqnData", "version": ">= 0.99.3", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "networkinference", "graphandnetwork", "normalization" ], "_stars": 5, "_contributors": [ { "user": "yiwang12", "count": 303, "uuid": 37149810 }, { "user": "kasperdanielhansen", "count": 44, "uuid": 4956575 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 324, "source": "https://www.bioconductor.org/packages/stats/bioc/spqn" }, "_devurl": "https://github.com/hansenlab/spqn", "_searchresults": 30, "_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/spqn.html", "manual.pdf" ], "_homeurl": "https://github.com/hansenlab/spqn", "_realowner": "bioc", "_cranurl": false, "_exports": [ "get_IQR_condition_exp", "normalize_correlation", "plot_IQR_condition_exp", "plot_signal_condition_exp", "qqplot_condition_exp" ], "_help": [ { "page": "spqn-package", "title": "Spatial quantile normalization", "topics": [ "spqn-package", "spqn" ] }, { "page": "normalize_correlation", "title": "Spatial quantile normalization (SpQN)", "topics": [ "normalize_correlation" ] }, { "page": "plot_IQR_condition_exp", "title": "Get and plot the IQRs of submatrices of the correlation matrix.", "topics": [ "get_IQR_condition_exp", "plot_IQR_condition_exp" ] }, { "page": "plot_signal_condition_exp", "title": "Plot the signal and background distribution of a correlation matrix.", "topics": [ "plot_signal_condition_exp" ] }, { "page": "qqplot_condition_exp", "title": "Q-Q plot for examing the distributions across submatrices of a correlation matrix.", "topics": [ "qqplot_condition_exp" ] } ], "_readme": "https://github.com/bioc/spqn/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "ggridges", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "R6", "RColorBrewer", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "spqn.Rmd", "filename": "spqn.html", "title": "Spatial quantile normalization for co-expression analysis", "author": "Yi Wang, Kasper D. Hansen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preliminaries", "Preparing your own data", "Examine the mean-correlation relationship", "Using SpQN to remove mean-correlation relationship", "Assess the impact of normalization", "SessionInfo", "References" ], "created": "2019-10-13 01:30:05", "modified": "2020-04-13 14:04:59", "commits": 55 } ], "_score": 5.176091259055681, "_indexed": true, "_nocasepkg": "spqn", "_universes": [ "bioc", "hansenlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-26T06:05:14.000Z", "distro": "noble", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "c6b1db2525fee5c0d170bb5985bb8e579f9785145e9bfd6a1a683b49408e81a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-26T06:05:20.000Z", "distro": "noble", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "96e266ca9c0b0ff43fe4fb2ddbc4bfcf30d5380ff9484c04a90f548838142517", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-26T06:04:16.000Z", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "d1d9d25e86530313af0224ab7232a541544bdcbd7104efb4790ee4e7a108a951", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-26T06:04:24.000Z", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "9b1a3d399a5addf079cc8180fca5b85f06ea11d0451c04235a8ba43806f93f94", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-26T06:05:08.000Z", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "2f99a8ad39a8ded4337721f9991e08d777a15592364e7dd2951f7479c85d5755", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-26T06:04:12.000Z", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "d22e42c16a920cfc7f73b12b4f23214459073142ae87fffef58495d70845b65c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-26T06:04:15.000Z", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "f45da5c890009440c1b347199d2228b1df8aee29179d47d11caf4708a25d824c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-26T06:04:12.000Z", "commit": "fb7533c4850a9714fa830599a5dd38474d8954aa", "fileid": "d7eaeaa3e7d3d0786cd0851e5a90e82fb841eefa4269f1e2bec5fdde52006891", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435132022" } ] }