{ "_id": "6a324eed3efcd9bda437d0c5", "Package": "HGC", "Type": "Package", "Title": "A fast hierarchical graph-based clustering method", "Version": "1.20.0", "Authors@R": "c(person(\"Zou\", \"Ziheng\",\nemail = \"zouzh14@gmail.com\",\nrole=c(\"aut\")),\nperson(\"Hua\", \"Kui\",\nrole=c(\"aut\")),\nperson(\"XGlab\",\nemail = \"xglab@mail.tsinghua.edu.cn\",\nrole=c(\"cre\", \"cph\")))", "Description": "HGC (short for Hierarchical Graph-based Clustering) is an\nR package for conducting hierarchical clustering on large-scale\nsingle-cell RNA-seq (scRNA-seq) data. The key idea is to\nconstruct a dendrogram of cells on their shared nearest\nneighbor (SNN) graph. HGC provides functions for building\ngraphs and for conducting hierarchical clustering on the graph.\nThe users with old R version could visit\nhttps://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get\nHGC package built for R 3.6.", "License": "GPL-3", "Encoding": "UTF-8", "SystemRequirements": "C++11", "VignetteBuilder": "knitr", "biocViews": "SingleCell, Software, Clustering, RNASeq, GraphAndNetwork,\nDNASeq", "Config/testthat/edition": "3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-17 07:27:45 UTC", "User": "root" }, "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:56:04 UTC", "RemoteUrl": "https://github.com/bioc/HGC", "RemoteRef": "RELEASE_3_23", "RemoteSha": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "Author": "Zou Ziheng [aut],\nHua Kui [aut],\nXGlab [cre, cph]", "Maintainer": "XGlab ", "MD5sum": "2178930bdb1015e2241bec8aaa2b22f3", "_user": "bioc-release", "_type": "src", "_file": "HGC_1.20.0.tar.gz", "_fileid": "7d977f4b01221b961140fdde77af681d1960b5c6381e429640f0adadf01b563a", "_filesize": 458914, "_sha256": "7d977f4b01221b961140fdde77af681d1960b5c6381e429640f0adadf01b563a", "_created": "2026-06-17T07:27:45.000Z", "_published": "2026-06-17T07:38:21.307Z", "_jobs": [ { "job": 81841612080, "time": 257, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7688799790" }, { "job": 81841612148, "time": 248, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7688797044" }, { "job": 81841612177, "time": 289, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7688809906" }, { "job": 81841612157, "time": 258, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7688799916" }, { "job": 81841612178, "time": 301, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7688815470" }, { "job": 81841612143, "time": 216, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7688786916" }, { "job": 81841612221, "time": 504, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7688876995" }, { "job": 81841612225, "time": 200, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7688782574" }, { "job": 81841612170, "time": 444, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7688858047" }, { "job": 81840787779, "time": 306, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7688718971" }, { "job": 81841612159, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7688762143" }, { "job": 81841612163, "time": 291, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7688810297" }, { "job": 81841612200, "time": 245, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7688796338" }, { "job": 81841612133, "time": 248, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7688797931" } ], "_bioccheck": { "error": 0, "warning": 3, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/HGC", "_commit": { "id": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380964 }, "_maintainer": { "name": "XGlab", "email": "xglab@mail.tsinghua.edu.cn" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "RcppEigen", "version": ">= 0.3.2.0", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "RANN", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "dendextend", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "software", "clustering", "rnaseq", "graphandnetwork", "dnaseq", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_searchresults": 29, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HGC.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "CKNN.Construction", "FindClusteringTree", "HGC.dendrogram", "HGC.parameter", "HGC.PlotARIs", "HGC.PlotDendrogram", "HGC.PlotParameter", "KNN.Construction", "MST.Construction", "PMST.Construction", "RNN.Construction", "SNN.Construction" ], "_datasets": [ { "name": "Pollen", "title": "Embeddings of the Pollen datasets in the principal component space.", "object": "Pollen", "file": "Pollen.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "CKNNConstruction", "title": "Building Unweighted Continuous K Nearest Neighbor Graph", "topics": [ "CKNN.Construction" ] }, { "page": "RAPI_FindClusteringTree", "title": "The HGC algorithm embedded in Seurat pipeline", "topics": [ "FindClusteringTree" ] }, { "page": "RHGC", "title": "Hierarchical Graph-based Clustering", "topics": [ "HGC.dendrogram" ] }, { "page": "RTime", "title": "Recording the Parameters of the Graph-based Hierarchical Clustering", "topics": [ "HGC.parameter" ] }, { "page": "RHGCPlotARIs", "title": "Calculating and Visualizing ARIs of the clustering results with given labels", "topics": [ "HGC.PlotARIs" ] }, { "page": "RHGCPlotDendrogram", "title": "Visualizing the dendrogram", "topics": [ "HGC.PlotDendrogram" ] }, { "page": "RHGCPlotParameter", "title": "Visualizing the Parameter Records during Clustering", "topics": [ "HGC.PlotParameter" ] }, { "page": "KNNConstruction", "title": "Building Unweighted K Nearest Neighbor Graph", "topics": [ "KNN.Construction" ] }, { "page": "MSTConstruction", "title": "Building Unweighted Minimum Spanning Tree Graph", "topics": [ "MST.Construction" ] }, { "page": "PMSTConstruction", "title": "Building Unweighted Perturbed Minimum Spanning Tree Graph", "topics": [ "PMST.Construction" ] }, { "page": "Pollen", "title": "Embeddings of the Pollen datasets in the principal component space.", "topics": [ "Pollen" ] }, { "page": "RNNConstruction", "title": "Building Unweighted epsilon Nearest Neighbor Graph", "topics": [ "RNN.Construction" ] }, { "page": "SNNConstruction", "title": "Building Unweighted Shared Nearest Neighbor Graph", "topics": [ "SNN.Construction" ] } ], "_readme": "https://github.com/bioc/HGC/raw/RELEASE_3_23/README.md", "_rundeps": [ "ape", "cli", "cpp11", "dendextend", "digest", "dplyr", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "mclust", "nlme", "patchwork", "pillar", "pkgconfig", "R6", "RANN", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridis", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "HGC.Rmd", "filename": "HGC.html", "title": "HGC package manual", "author": "Zou Ziheng, Hua Kui", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick Start", "Input data", "Run HGC", "Run HGC with existing scRNA-seq data processing pipelines", "Seurat pipeline", "scran pipeline", "Visualization", "Evaluation of the clustering results", "Time complexity analysis of HGC" ], "created": "2021-04-10 02:55:27", "modified": "2021-06-13 16:34:45", "commits": 5 } ], "_score": 4.763427993562938, "_indexed": false, "_nocasepkg": "hgc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/HGC", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-06-17T07:31:29.000Z", "distro": "noble", "arch": "aarch64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "866efa2f9fdae48e7cbeeea7e37c0d1e47f70cc69dccc85e29ad07bab74da8ca", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-06-17T07:31:54.000Z", "distro": "noble", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "5be4bed7641fe428566aefb507af955ef129e693e265f0e81f398524841c307f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-06-17T07:31:40.000Z", "distro": "noble", "arch": "aarch64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "4ba309b47c4ce1b36b16f18130fcb95d8cda4c09f65d550b095b2f271c8a8069", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-06-17T07:32:23.000Z", "distro": "noble", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "d1a0a34e2bd193e3d3f1f07da0bcd36327d5700f45bd4d21801a59c509f844d8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-06-17T07:31:12.000Z", "arch": "aarch64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "fb975d9c7c025ee7ff78f8ae5e4ac8d23d1edb9982a7344f9de105fde090d18e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-06-17T07:32:53.000Z", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "1400a3f0e636bbd3f73b989c012dee5cbb8970d09a94dec5d91f2c3e3e95ad1f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-06-17T07:31:01.000Z", "arch": "aarch64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "b54ee0a612715206228e9f72932d87aec5a27d6a023ba0568a10901632ddb838", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-06-17T07:31:43.000Z", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "2a54f6d92a60d5122710aecbe1603b18ef608c813b70ff29be056ddc4069fb7e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-06-17T07:31:29.000Z", "arch": "emscripten", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "991ec45dbeb9ebc8a552e6b10073690c7eb8b0ed808d6f33fc807844539f393d", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-06-17T07:31:05.000Z", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "70cf1478da66b0d2e38ac7d6152bce1097c3ba6c77e313cde82ff135c2ed5bf1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-06-17T07:30:28.000Z", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "8b6d094d1b6959c252b8eee2886624f95b21ebd602f442ea3571abbe4deed6ca", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-06-17T07:30:39.000Z", "arch": "x86_64", "commit": "4afcd45b87dcf62713b2b4b9674d275c98df8852", "fileid": "779ee910c3f2e2919ef1bf895391ec255be3061707c0e5d745c657b7829ef323", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27672765858" } ] }