{ "_id": "6a10fbd4acfb0bcc41ce136d", "Package": "scPharm", "Title": "Identification of Pharmacological Subpopulations of Single Cells\nfor Precision Medicine in Cancers", "Version": "1.0.6", "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\")),\nperson(\"Peng\", \"Tian\", email = \"2131443@tongji.edu.cn\", role = c(\"aut\", \"ctb\")),\nperson(\"Jie\", \"Zheng\", email = \"2210791@tongji.edu.cn\", role = c(\"aut\", \"ctb\")),\nperson(\"Haiyun\", \"Wang\", email = \"wanghaiyun@tongji.edu.cn\", role = c(\"aut\", \"ctb\")))", "Description": "A computational framework for single-cell RNA-seq data\nthat integrates pharmacogenomics profiles to uncover\ntherapeutic heterogeneity within tumors at single-cell\nresolution. The tool prioritizes tailored drugs and provides\ninsights into combination therapy regimens and drug toxicity in\ncancers.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "LazyData": "true", "LazyDataCompression": "xz", "URL": "https://github.com/Zaoqu-Liu/scPharm,\nhttps://zaoqu-liu.github.io/scPharm/", "BugReports": "https://github.com/Zaoqu-Liu/scPharm/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev python3\nzlib1g-dev", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-25 06:49:56 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/scPharm", "RemoteRef": "main", "RemoteSha": "33a25f64d3748973d513bcdadb2c32a18c048064", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-04-25 09:24:56 UTC", "User": "root" }, "Author": "Zaoqu Liu [aut, cre] (ORCID: ),\nPeng Tian [aut, ctb],\nJie Zheng [aut, ctb],\nHaiyun Wang [aut, ctb]", "Maintainer": "Zaoqu Liu ", "MD5sum": "56c49f853d74c1df9379eb8d46862693", "_user": "zaoqu-liu", "_type": "src", "_file": "scPharm_1.0.6.tar.gz", "_fileid": "0b20899affef944dfbc19f580bc2b616b63ac6d1ab7f09ef60c57b409377e72e", "_filesize": 66138410, "_sha256": "0b20899affef944dfbc19f580bc2b616b63ac6d1ab7f09ef60c57b409377e72e", "_created": "2026-04-25T09:24:56.000Z", "_distro": "noble", "_jobs": [ { "job": 77483988544, "time": 663, "config": "linux-devel-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6639070141" }, { "job": 77483988667, "time": 749, "config": "linux-devel-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6639076976" }, { "job": 77483988657, "time": 686, "config": "linux-release-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6639072080" }, { "job": 77483988647, "time": 687, "config": "linux-release-x86_64", "r": 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"NOTE", "artifact": "6639068590" }, { "job": 77483988653, "time": 646, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6639068815" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/24927578342", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/scPharm", "_commit": { "id": "33a25f64d3748973d513bcdadb2c32a18c048064", "author": "Zaoqu-Liu ", "committer": "Zaoqu-Liu ", "message": "fix: Windows compatibility for CNV analysis\n\n- Add .safe_parDist() wrapper for parallelDist::parDist()\n - Uses base R dist() on Windows to avoid OpenMP crashes\n - Falls back to dist() if parallelDist fails on any platform\n\n- Add .safe_mclapply() wrapper for parallel::mclapply()\n - Uses sequential lapply() on Windows (fork not supported)\n - Uses mclapply() on Unix/Mac with multiple cores\n\nThis fixes R session crash on Windows when running\nDoPharmID.scPharm() with type=\"tissue\" (CNV analysis).\n\nCloses: Windows fatal error during [CNV] Computing baseline\n", "time": 1769323796 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "orcid": "0000-0002-0452-742X", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Seurat", "version": ">= 4.0.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "CelliD", "role": "Imports" }, { "package": "SeuratObject", "role": "Imports" }, { "package": "fgsea", "version": ">= 1.16.0", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "mixtools", "version": ">= 2.0.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.2", "role": "Imports" }, { "package": "sparseMatrixStats", "version": ">= 1.2.1", "role": "Imports" }, { "package": "irlba", "version": ">= 2.3.5.1", "role": "Imports" }, { "package": "tidyr", "version": ">= 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Threshold Calibration with Normal Tissue", "Using scPharmGenNullDist", "Apply Calibrated Thresholds", "Threshold Selection Strategy", "2. Multi-Drug Analysis", "Pan-Drug Screening", "Drug Class Analysis", "Multi-Cancer Analysis", "3. Combination Therapy Optimization", "scPharmCombo Analysis", "Combination Selection Criteria", "4. Integration with Seurat Workflows", "Pre-computed Embeddings", "Cluster-Level Analysis", "5. Performance Tuning", "Memory Management", "Parallel Processing", "Parameter Optimization", "6. Custom Drug Signatures", "Using External Gene Sets", "7. Quality Control", "Pre-analysis Checks", "Post-analysis Validation", "8. Troubleshooting", "Common Issues", "Debug Mode", "9. 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