{ "_id": "6a211e80cd65a98ecbd1e046", "Package": "PopComm", "Title": "Population-Level Cell-Cell Communication Analysis Tools", "Version": "1.0.1", "Authors@R": "c(person(given = \"Zheng\", family = \"Gong\", email = \"gongzheng131@hotmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7285-2630\")),\nperson(given = \"Mengwei\", family = \"Li\", email = \"limengwei833@gmail.com\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0001-6163-2827\")))", "Description": "Facilitates population-level analysis of ligand-receptor\n(LR) interactions using large-scale single-cell transcriptomic\ndata. Identifies significant LR pairs and quantifies their\ninteractions through correlation-based filtering and projection\nscore computations. Designed for large-sample single-cell\nstudies, the package employs statistical modeling, including\nlinear regression, to investigate LR relationships between cell\ntypes. It provides a systematic framework for understanding\ncell-cell communication, uncovering regulatory interactions and\nsignaling mechanisms. Offers tools for LR pair-level,\nsample-level, and differential interaction analyses, with\ncomprehensive visualization support to aid biological\ninterpretation. The methodology is described in a manuscript\ncurrently under review and will be referenced here once\npublished or publicly available.", "URL": "https://github.com/JusticeGO/PopComm", "BugReports": "https://github.com/JusticeGO/PopComm/issues", "biocViews": "", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "LazyData": "true", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://justicego.r-universe.dev", "Date/Publication": "2026-02-04 09:00:31 UTC", "RemoteUrl": "https://github.com/justicego/popcomm", "RemoteRef": "HEAD", "RemoteSha": "6e4d7ba83582b8d57d70e4ae2b5ea1a567768e38", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 06:38:11 UTC", "User": "root" }, "Author": "Zheng Gong [aut, cre] (ORCID: ),\nMengwei Li [aut, ctb] (ORCID: )", "Maintainer": "Zheng Gong ", "MD5sum": "726a18aa6493383d2752177a56a2d062", "_user": "justicego", "_type": "src", "_file": "PopComm_1.0.1.tar.gz", "_fileid": "233a912d6d643ba2c949b7c903527eb406b13878103c224beae219e2a5f9f9f8", "_filesize": 2712128, "_sha256": "233a912d6d643ba2c949b7c903527eb406b13878103c224beae219e2a5f9f9f8", "_created": "2026-06-04T06:38:11.000Z", "_published": "2026-06-04T06:43:12.900Z", "_distro": "noble", "_jobs": [ { "job": 79463701011, "time": 217, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7404737621" }, { "job": 79463701028, "time": 227, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7404740313" }, { "job": 79463701014, "time": 262, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7404738693" }, { "job": 79463700999, "time": 232, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7404731909" }, { "job": 79463160516, "time": 248, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7404676585" }, { "job": 79463700998, "time": 176, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7404726207" }, { "job": 79463701018, "time": 147, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7404718437" }, { "job": 79463701043, "time": 144, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7404717375" }, { "job": 79463701051, "time": 147, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7404718144" } ], "_buildurl": "https://github.com/r-universe/justicego/actions/runs/26935177840", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/justicego/popcomm", "_commit": { "id": "6e4d7ba83582b8d57d70e4ae2b5ea1a567768e38", "author": "GongZ <1243287088@qq.com>", "committer": "GongZ <1243287088@qq.com>", "message": "update v1.0.1\n", "time": 1770195631 }, "_maintainer": { "name": "Zheng Gong", "email": "gongzheng131@hotmail.com", "orcid": "0000-0001-7285-2630" }, "_registered": 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{ "user": "justicego", "count": 93, "uuid": 41421539 } ], "_userbio": { "uuid": 41421539, "type": "user", "name": "GongZ" }, "_downloads": { "count": 142, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PopComm" }, "_devurl": "https://github.com/justicego/popcomm", "_searchresults": 1, "_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/PopComm.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/justicego/popcomm", "_realowner": "justicego", "_cranurl": true, "_releases": [ { "version": "0.1.0.1", "date": "2025-04-25" }, { "version": "1.0.0", "date": "2025-11-01" } ], "_exports": [ "boxplot_lr_group_comparison", "circle_plot", "dot_plot", "dotplot_lr_continuous_group", "filter_lr_all", "filter_lr_single", "heatmap_sample", "lr_linear_model_discrete", "one_step_all", "one_step_single", "pca_sample", "score_lr_all", "score_lr_single" ], "_datasets": [ { "name": "filtered_lr_eg", "title": "Example for filtered_lr", "object": "filtered_lr_eg", "class": [ "data.frame" ], "fields": [ "ligand", "receptor", "cor", "p_val", "adjust.p", "sender", "receiver", "slope", "intercept", "r2", "fstat" ], "rows": 1513, "table": true, "tojson": true }, { "name": "lr_db", "title": "Ligand-Receptor Pair Database", "object": "lr_db", "class": [ "data.frame" ], "fields": [ "lr_pair", "ligand_gene_symbol", "receptor_gene_symbol", "ligand_gene_id", "receptor_gene_id", "ligand_ensembl_protein_id", "receptor_ensembl_protein_id", "ligand_ensembl_gene_id", "receptor_ensembl_gene_id", "evidence" ], "rows": 3398, "table": true, "tojson": true }, { "name": "lr_scores_eg", "title": "Example for lr_scores", "object": "lr_scores_eg", "class": [ "data.frame" ], "fields": [ "ligand", "receptor", "cor", "p_val", "adjust.p", "sender", "receiver", "slope", "intercept", "r2", "fstat", "sample", "score", "normalized_score" ], "rows": 187593, "table": true, "tojson": true }, { "name": "matrix_object", "title": "Example for matrix object", "object": "matrix_object", "class": [ "matrix", "array" ], "fields": [ "Endothelial--GSM4850581", "Endothelial--GSM5572757", "Endothelial--GSM5572758", "Endothelial--GSM5572759", "Endothelial--GSM5572760", "Endothelial--GSM5572763", "Endothelial--GSM6720563", "Endothelial--GSM6720564", "Endothelial--GSM6720565", "Endothelial--GSM6720566", "Endothelial--GSM6720567", "Endothelial--GSM6720568", "Endothelial--GSM6720569", "Endothelial--GSM6720570", "Endothelial--GSM6720571", "Endothelial--GSM6720572", "Endothelial--GSM6720573", "Endothelial--GSM6720574", "Endothelial--GSM6720575", "Endothelial--GSM6720576", "Endothelial--GSM6720577", "Endothelial--GSM6720578", "Endothelial--GSM6720579", "Endothelial--GSM6720580", "Endothelial--GSM6720581", "Endothelial--GSM6720582", "Endothelial--GSM6720583", "Endothelial--HCAHeart7656534", "Endothelial--HCAHeart7656535", "Endothelial--HCAHeart7656536", "Endothelial--HCAHeart7656538", "Endothelial--HCAHeart7728606", "Endothelial--HCAHeart7745966", "Endothelial--HCAHeart7745967", "Endothelial--HCAHeart7745968", "Endothelial--HCAHeart7745969", "Endothelial--HCAHeart7745970", "Endothelial--HCAHeart7751845", "Endothelial--HCAHeart7843999", "Endothelial--HCAHeart7844000", "Endothelial--HCAHeart7844001", "Endothelial--HCAHeart7844002", "Endothelial--HCAHeart7844003", "Endothelial--HCAHeart7844004", "Endothelial--HCAHeart7850539", "Endothelial--HCAHeart7850540", "Endothelial--HCAHeart7850541", "Endothelial--HCAHeart7850542", "Endothelial--HCAHeart7850543", "Endothelial--HCAHeart7850544", "Endothelial--HCAHeart7850545", "Endothelial--HCAHeart7850546", "Endothelial--HCAHeart7850547", "Endothelial--HCAHeart7850548", "Endothelial--HCAHeart7850549", "Endothelial--HCAHeart7850551", "Endothelial--HCAHeart7905327", "Endothelial--HCAHeart7905328", "Endothelial--HCAHeart7905329", "Endothelial--HCAHeart7905330", "Endothelial--HCAHeart7905331", "Endothelial--HCAHeart7905332", "Endothelial--HCAHeart8102858", "Endothelial--HCAHeart8102859", "Endothelial--HCAHeart8102860", "Endothelial--HCAHeart8102861", "Endothelial--HCAHeart8102862", "Endothelial--HCAHeart8102863", "Endothelial--HCAHeart8102865", "Endothelial--HCAHeart8102866", "Endothelial--HCAHeart8102867", "Endothelial--HCAHeart8102868", "Perivascular--GSM4850581", "Perivascular--GSM5572757", "Perivascular--GSM5572758", "Perivascular--GSM5572759", "Perivascular--GSM5572760", "Perivascular--GSM5572763", "Perivascular--GSM6720563", "Perivascular--GSM6720564", "Perivascular--GSM6720565", "Perivascular--GSM6720566", "Perivascular--GSM6720567", "Perivascular--GSM6720568", "Perivascular--GSM6720569", "Perivascular--GSM6720570", "Perivascular--GSM6720571", "Perivascular--GSM6720572", "Perivascular--GSM6720573", "Perivascular--GSM6720574", "Perivascular--GSM6720575", "Perivascular--GSM6720576", "Perivascular--GSM6720577", "Perivascular--GSM6720578", "Perivascular--GSM6720579", "Perivascular--GSM6720580", "Perivascular--GSM6720581", "Perivascular--GSM6720582", "Perivascular--GSM6720583", "Perivascular--HCAHeart7656534", "Perivascular--HCAHeart7656535", "Perivascular--HCAHeart7656536", "Perivascular--HCAHeart7656538", "Perivascular--HCAHeart7728606", "Perivascular--HCAHeart7745966", "Perivascular--HCAHeart7745967", "Perivascular--HCAHeart7745968", "Perivascular--HCAHeart7745969", "Perivascular--HCAHeart7745970", "Perivascular--HCAHeart7751845", "Perivascular--HCAHeart7843999", "Perivascular--HCAHeart7844000", "Perivascular--HCAHeart7844001", "Perivascular--HCAHeart7844002", "Perivascular--HCAHeart7844003", "Perivascular--HCAHeart7844004", "Perivascular--HCAHeart7850539", "Perivascular--HCAHeart7850540", "Perivascular--HCAHeart7850541", "Perivascular--HCAHeart7850542", "Perivascular--HCAHeart7850543", "Perivascular--HCAHeart7850544", "Perivascular--HCAHeart7850545", "Perivascular--HCAHeart7850546", "Perivascular--HCAHeart7850547", "Perivascular--HCAHeart7850548", "Perivascular--HCAHeart7850549", "Perivascular--HCAHeart7850551", "Perivascular--HCAHeart7905327", "Perivascular--HCAHeart7905328", "Perivascular--HCAHeart7905329", "Perivascular--HCAHeart7905330", "Perivascular--HCAHeart7905331", "Perivascular--HCAHeart7905332", "Perivascular--HCAHeart8102858", "Perivascular--HCAHeart8102859", "Perivascular--HCAHeart8102860", "Perivascular--HCAHeart8102861", "Perivascular--HCAHeart8102862", "Perivascular--HCAHeart8102863", "Perivascular--HCAHeart8102865", "Perivascular--HCAHeart8102866", "Perivascular--HCAHeart8102867", "Perivascular--HCAHeart8102868" ], "rows": 223, "table": true, "tojson": true }, { "name": "metadata_eg", "title": "Example for metadata", "object": "metadata_eg", "class": [ "data.frame" ], "fields": [ "sample", "Project", "Age_imputation", "Age_range_normalized", "Age_group", "Sex", "Standardized_region", "IFNscore", "IFN_type" ], "rows": 163, "table": true, "tojson": true } ], "_help": [ { "page": "boxplot_lr_group_comparison", "title": "Boxplot Comparison of Ligand-Receptor Interaction Scores Across Groups", "topics": [ "boxplot_lr_group_comparison" ] }, { "page": "circle_plot", "title": "Plot Circular Ligand-Receptor Interaction Network", "topics": [ "circle_plot" ] }, { "page": "dot_plot", "title": "Create Ligand-Receptor Interaction Dot Plot", "topics": [ "dot_plot" ] }, { "page": "dotplot_lr_continuous_group", "title": "Dotplot of Ligand-Receptor Interaction Scores Against Continuous Group Variable", "topics": [ "dotplot_lr_continuous_group" ] }, { "page": "filter_lr_all", "title": "Filter and Analyze Ligand-Receptor Pair Correlations (All Cell Types)", "topics": [ "filter_lr_all" ] }, { "page": "filter_lr_single", "title": "Filter and Analyze Ligand-Receptor Pair Correlations (Specified Sender and Receiver)", "topics": [ "filter_lr_single" ] }, { "page": "filtered_lr_eg", "title": "Example for filtered_lr", "topics": [ "filtered_lr_eg" ] }, { "page": "heatmap_sample", 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