{ "_id": "6a587040ff0138dec5d73681", "Package": "hoodscanR", "Title": "Spatial cellular neighbourhood scanning in R", "Version": "1.11.0", "Authors@R": "c(person(given = \"Ning\",\nfamily = \"Liu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ning.liu@adelaide.edu.au\",\ncomment = c(ORCID = \"0000-0002-9487-9305\")),\nperson(given = \"Jarryd\",\nfamily = \"Martin\",\nrole = c(\"aut\"),\nemail = \"\",\ncomment = c(ORCID = \"\")))", "Description": "hoodscanR is an user-friendly R package providing\nfunctions to assist cellular neighborhood analysis of any\nspatial transcriptomics data with single-cell resolution. All\nfunctions in the package are built based on the\nSpatialExperiment object, allowing integration into various\nspatial transcriptomics-related packages from Bioconductor. The\npackage can result in cell-level neighborhood annotation\noutput, along with funtions to perform neighborhood\ncolocalization analysis and neighborhood-based cell clustering.", "biocViews": "Spatial, Transcriptomics, SingleCell, Clustering", "License": "GPL-3 + file LICENSE", "URL": "https://github.com/DavisLaboratory/hoodscanR,\nhttps://davislaboratory.github.io/hoodscanR/", "BugReports": "https://github.com/DavisLaboratory/hoodscanR/issues", "Encoding": "UTF-8", "LazyData": "false", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libicu-dev\nlibpng-dev libuv1-dev libssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:29 UTC", "RemoteUrl": "https://github.com/bioc/hoodscanR", "RemoteRef": "HEAD", "RemoteSha": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-16 05:21:24 UTC", "User": "root" }, "Author": "Ning Liu [aut, cre] (ORCID: ),\nJarryd Martin [aut]", "Maintainer": "Ning Liu ", "_user": "bioc", "_type": "src", "_file": "hoodscanR_1.11.0.tar.gz", "_fileid": "https://r2.ropensci.org/10033a6d22ade92cf431497a6b363902fae5b0328172270c8d6f5e7eede69fb8", "_filesize": 2872484, "_sha256": "10033a6d22ade92cf431497a6b363902fae5b0328172270c8d6f5e7eede69fb8", "_expires": "2026-10-24T05:46:38.000Z", "_created": "2026-07-16T05:21:24.000Z", "_published": "2026-07-16T05:46:39.987Z", "_bioccheck": { "error": 0, "warning": 1, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678", "_status": "success", "_upstream": "https://github.com/bioc/hoodscanR", "_commit": { "id": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381289 }, "_maintainer": { "name": "Ning Liu", "email": "ning.liu@adelaide.edu.au", "login": "ningbioinfo", "linkedin": "in/ning-liu-437617157", "description": "Bioinformatician @ Polo Lab, Univ. of Adelaide · spatial & single-cell genomics, epigenomics, deep learning · standR / hoodscanR / scider", "uuid": 13725215, "orcid": "0000-0002-9487-9305" }, "_distro": "resolute", "_jobs": [ { "job": 87542070559, "time": 194, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8365777278" }, { "job": 87542070602, "time": 282, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8365800791" }, { "job": 87542070565, "time": 393, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8365829126" }, { "job": 87542070569, "time": 293, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8365803759" }, { "job": 87542070612, "time": 407, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8365832882" }, { "job": 87542070545, "time": 177, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8366106903" }, { "job": 87542070514, "time": 426, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8365849106" }, { "job": 87542070517, "time": 287, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8366113827" }, { "job": 87542070554, "time": 596, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8365904685" }, { "job": 87541419908, "time": 264, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8365724982" }, { "job": 87542070519, "time": 161, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8365768535" }, { "job": 87542070498, "time": 266, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8365795831" }, { "job": 87542070512, "time": 254, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8365793101" }, { "job": 87542070492, "time": 270, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8365797369" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "knitr", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "scico", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "RANN", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.9", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.11.0", "bioc": "3.24" }, { "branch": "release", "version": "1.10.0", "bioc": "3.23" } ], "_topics": [ "spatial", "transcriptomics", "singlecell", "clustering", "cpp" ], "_stars": 13, "_contributors": [ { "user": "ningbioinfo", "count": 48, "uuid": 13725215 }, { "user": "jwokaty", "count": 3, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 447, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 358, "source": "https://www.bioconductor.org/packages/stats/bioc/hoodscanR" }, "_devurl": "https://github.com/davislaboratory/hoodscanr", "_pkgdown": "https://davislaboratory.github.io/hoodscanR/", "_searchresults": 38, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hoodscanR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/davislaboratory/hoodscanr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calcMetrics", "clustByHood", "findNearCells", "mergeByGroup", "mergeHoodSpe", "perplexityPermute", "plotColocal", "plotHoodMat", "plotProbDist", "plotTissue", "readHoodData", "scanHoods" ], "_datasets": [ { "name": "spe", "title": "Example test spatial transcriptomics data", "object": "spe_test", "file": "spe_test.rda", "class": [ "SpatialExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "calcMetrics", "title": "Calculate metrics for probability matrix", "topics": [ "calcMetrics" ] }, { "page": "clustByHood", "title": "Cluster the probability matrix with K-means", "topics": [ "clustByHood", "clustByHood,matrix-method", "clustByHood,SpatialExperiment-method" ] }, { "page": "findNearCells", "title": "Find the k-th nearest cells for each cell", "topics": [ "findNearCells" ] }, { "page": "mergeByGroup", "title": "Merge probability matrix based on annotations", "topics": [ "mergeByGroup" ] }, { "page": "mergeHoodSpe", "title": "Merge probability matrix into SpatialExperiment object.", "topics": [ "mergeHoodSpe" ] }, { "page": "perplexityPermute", "title": "Compute p-value for perplexity via permutation", "topics": [ "perplexityPermute" ] }, { "page": "plotColocal", "title": "Plot heatmap for neighbourhood analysis", "topics": [ "plotColocal", "plotColocal,matrix-method", "plotColocal,SpatialExperiment-method" ] }, { "page": "plotHoodMat", "title": "Plot probability matrix as a heatmap", "topics": [ "plotHoodMat", "plotHoodMat,matrix-method", "plotHoodMat,SpatialExperiment-method" ] }, { "page": "plotProbDist", "title": "Plot probability distribution", "topics": [ "plotProbDist", "plotProbDist,matrix-method", "plotProbDist,SpatialExperiment-method" ] }, { "page": "plotTissue", "title": "Plot cells based on cell position on tissue.", "topics": [ "plotTissue" ] }, { "page": "readHoodData", "title": "Read cellular position and annotation data into a list object.", "topics": [ "readHoodData" ] }, { "page": "scanHoods", "title": "Scan cellular neighbourhoods.", "topics": [ "scanHoods" ] } ], "_readme": "https://github.com/bioc/hoodscanR/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "Biobase", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "bslib", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "digest", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "fs", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "GlobalOptions", "glue", "gtable", "highr", "htmltools", "httr2", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "rjson", "rlang", "rmarkdown", "RSQLite", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scico", "Seqinfo", "shape", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "Quick_start.Rmd", "filename": "Quick_start.html", "title": "A quick start guide to the hoodscanR package", "author": "Ning Liu, Melissa Davis", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick start", "Data exploration", "Neighborhoods scanning", "Neighborhoods analysis", "Session info" ], "created": "2023-08-14 11:02:47", "modified": "2023-09-25 06:18:52", "commits": 4 } ], "_score": 5.693726948923647, "_indexed": true, "_nocasepkg": "hoodscanr", "_universes": [ "bioc", "ningbioinfo", "davislaboratory" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.11.0", "date": "2026-07-16T05:24:45.000Z", "distro": "resolute", "arch": "aarch64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/b8f293a18ed88ee52ea10419844dd3dfa710c8bd0aa5da34c49d7678c1b152d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.7.0", "os": "linux", "version": "1.11.0", "date": "2026-07-16T05:25:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/d49102437c32838226ee33299531b2ac4c187e4e7cea590bba3e29edf5667a91", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.6.1", "os": "linux", "version": "1.11.0", "date": "2026-07-16T05:24:51.000Z", "distro": "resolute", "arch": "aarch64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/c5808577573964d73f62ac123aafaae6fe26f391a9c3930afa667e052bc6f534", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.6.1", "os": "linux", "version": "1.11.0", "date": "2026-07-16T05:26:09.000Z", "distro": "resolute", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/4b4dd7f6e99528c565c1a94f92a2a62ee3b9e70408836761527d3de9da4ba52d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.5.3", "os": "mac", "version": "1.11.0", "date": "2026-07-16T05:44:03.000Z", "arch": "aarch64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/fed1c199bfdcb5769284705b634d8479aebc3e05d926b78ec3e8f51e1590f088", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.5.3", "os": "mac", "version": "1.11.0", "date": "2026-07-16T05:25:28.000Z", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/009dc3765c797a25efa954bd7d7268521c85728040d657105c8cb90b6102f7ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.6.1", "os": "mac", "version": "1.11.0", "date": "2026-07-16T05:43:23.000Z", "arch": "aarch64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/104f8b8f2b66c8d29f6c430c2c94e48fb693db9f53136a0df5c1f2b872bc0839", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.6.1", "os": "mac", "version": "1.11.0", "date": "2026-07-16T05:27:47.000Z", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/dde981c1b7a83c8f87e2410b192fa6bd7d58ed44fe99877052bd399995014125", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.6.0", "os": "wasm", "version": "1.11.0", "date": "2026-07-16T05:24:35.000Z", "arch": "emscripten", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/6d02a76f6e103a2ddbf11a13dd7cd587c4b85e61ab3f95d4d2b7ad529a80fb56", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.7.0", "os": "win", "version": "1.11.0", "date": "2026-07-16T05:23:09.000Z", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/cbd80b10584595d8291f5b58fc4d22d1dba80ec433efa527b8816c9dad303548", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.5.3", "os": "win", "version": "1.11.0", "date": "2026-07-16T05:23:10.000Z", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/9685f081898a7c31aa8c07a8f366c8d792fb77e9d172863ecb6cca7de5e9a7e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" }, { "r": "4.6.1", "os": "win", "version": "1.11.0", "date": "2026-07-16T05:23:23.000Z", "arch": "x86_64", "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696", "fileid": "https://r2.ropensci.org/324ce88f7e304c5c3a88a1b2d7632831b1c915144155ea03f172c2f48c60f984", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473502678" } ] }