{ "_id": "6a156978acfb0bcc41d629b0", "Package": "NOVA", "Type": "Package", "Title": "Network Of Versatile Cell-Cell Communication Analysis", "Version": "1.0.0", "Date": "2026-01-26", "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"YOUR-ORCID-ID\")))", "Author": "Zaoqu Liu [aut, cre]", "Maintainer": "Zaoqu Liu ", "Description": "NOVA (Network Of Versatile cell-cell Analysis) is a\nhigh-performance R package for predicting and visualizing\ncell-to-cell communication networks from single-cell and bulk\ntranscriptomic data. It leverages connectomeDB2020, the most\ncomprehensive manually curated ligand-receptor interaction\ndatabase, to identify signaling interactions between cell\ntypes. NOVA features vectorized computations, parallel\nprocessing, and seamless integration with Seurat (V4/V5) for\nefficient analysis of large-scale datasets.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://zaoqu-liu.github.io/NOVA,\nhttps://github.com/Zaoqu-Liu/NOVA", "BugReports": "https://github.com/Zaoqu-Liu/NOVA/issues", "Config/testthat/edition": "3", "Collate": "'RcppExports.R' 'NOVA-package.R' 'globals.R' 'utils.R'\n'data.R' 'seurat_compat.R' 'extract_edges.R' 'diff_edges.R'\n'visualization.R' 'export.R' 'zzz.R'", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libpng-dev libxml2-dev perl", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-26 04:43:50 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/NOVA", "RemoteRef": "main", "RemoteSha": "be0787f27560a647a10b0dd60365f729a69ba396", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-26 09:28:12 UTC", "User": "root" }, "MD5sum": "6d2eea364577a09082672a1c653499cd", "_user": "zaoqu-liu", "_type": "src", "_file": "NOVA_1.0.0.tar.gz", "_fileid": "ddd64ff6fef774cc3557de69116307da7e3a95e7c02eb6cec649aac18d13c300", "_filesize": 7262617, "_sha256": "ddd64ff6fef774cc3557de69116307da7e3a95e7c02eb6cec649aac18d13c300", "_created": "2026-05-26T09:28:12.000Z", "_published": "2026-05-26T09:35:52.228Z", "_distro": "noble", "_jobs": [ { "job": 77845827524, "time": 206, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7213586070" }, { "job": 77845827506, "time": 220, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7213590658" }, { "job": 77845827677, "time": 213, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7213588375" }, { "job": 77845827678, "time": 222, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7213591287" }, { "job": 77845827449, "time": 99, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7213548238" }, { "job": 77845827511, "time": 410, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7213655811" }, { "job": 77845827607, "time": 151, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7213566083" }, { "job": 77845827476, "time": 407, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7213655054" }, { "job": 77845029834, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7213512348" }, { "job": 77845827497, "time": 179, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7213576644" }, { "job": 77845827398, "time": 265, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7213607103" }, { "job": 77845827373, "time": 200, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7213583960" }, { "job": 77845827523, "time": 184, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7213578365" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26443857381", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/NOVA", "_commit": { "id": "be0787f27560a647a10b0dd60365f729a69ba396", "author": "Zaoqu-Liu ", "committer": "Zaoqu-Liu ", "message": "Implement complete Python NATMI functionality in R NOVA\n\nNEW FEATURES:\n1. Export Functions (export.R):\n - ExportResults(): Comprehensive export with Excel conditional formatting\n - ExportLRPairs(): Individual files for each LR pair with color scales\n - Adjacency matrix export (count, mean, specificity)\n - README.txt with column descriptions\n\n2. DiffEdges Fill Missing Values:\n - Implements NATMI's complex missing value filling algorithm\n - When edge missing in one condition, fills ligand/receptor values\n from cluster_stats if gene is expressed\n - More accurate fold change calculations\n - New parameter: fill_missing = TRUE (default)\n\n3. Additional Visualizations:\n - PlotClusterComparison(): Bar plot comparing cluster sizes between conditions\n - PlotDotPlot(): Dot plot for LR pair expression across cluster pairs\n - PlotBubble(): Bubble chart summarizing communication\n - PlotCircos(): Enhanced circos plot (simplified version)\n - PlotLRNetwork(): Network for specific LR pair across all clusters\n\nFIXES:\n- Added median to stats imports\n- Added 'cluster' to globalVariables\n- Removed LazyData (no data directory)\n- Added Author/Maintainer fields to DESCRIPTION\n- Cleaned up build artifacts\n\nSTATUS:\n- R CMD check: 0 errors, 0 warnings, 2 notes (package size, timestamp)\n- All 125 tests passing\n- All new functions tested and working\n", "time": 1769402630 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", 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