{ "_id": "6a17eba2acfb0bcc41da36ec", "Package": "CytoProfile", "Title": "Cytokine Profiling Analysis Tool", "Version": "0.2.4", "Authors@R": "c(\nperson(\"Shubh\", \"Saraswat\", email = \"shubh.saraswat00@gmail.com\", role = c(\"cre\", \"aut\", \"cph\"),\ncomment = c(ORCID = \"0009-0009-2359-1484\")),\nperson(\"Xiaohua Douglas\", \"Zhang\", email = \"douglas.zhang@uky.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-2486-7931\")))", "Description": "Provides comprehensive cytokine profiling analysis through\nquality control using biologically meaningful cutoffs on raw\ncytokine measurements and by testing for distributional\nsymmetry to recommend appropriate transformations. Offers\nexploratory data analysis with summary statistics, enhanced\nboxplots, and barplots, along with univariate and multivariate\nanalytical capabilities for in-depth cytokine profiling such as\nPrincipal Component Analysis based on Andrzej Maćkiewicz and\nWaldemar Ratajczak (1993) ,\nSparse Partial Least Squares Discriminant Analysis based on Lê\nCao K-A, Boitard S, and Besse P (2011)\n, Random Forest based on Breiman,\nL. (2001) , and Extreme Gradient\nBoosting based on Tianqi Chen and Carlos Guestrin (2016)\n.", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/saraswatsh/CytoProfile,\nhttps://cytoprofile.cytokineprofile.org/", "NeedsCompilation": "no", "License": "GPL (>= 2)", "LazyData": "true", "VignetteBuilder": "knitr", "BugReports": "https://github.com/saraswatsh/CytoProfile/issues", "Language": "en-US", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nmake texlive libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev zlib1g-dev", "Repository": "https://saraswatsh.r-universe.dev", "Date/Publication": "2026-02-27 17:54:17 UTC", "RemoteUrl": "https://github.com/saraswatsh/cytoprofile", "RemoteRef": "HEAD", "RemoteSha": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "Packaged": { "Date": "2026-05-28 07:02:16 UTC", "User": "root" }, "Author": "Shubh Saraswat [cre, aut, cph] (ORCID:\n),\nXiaohua Douglas Zhang [aut] (ORCID:\n)", "Maintainer": "Shubh Saraswat ", "MD5sum": "a116e5af90e157cc490d3e119a4415fc", "_user": "saraswatsh", "_type": "src", "_file": "CytoProfile_0.2.4.tar.gz", "_fileid": "cef74a9d60092197dbfae4a34c83c1aa235b364163c15e721c7a594a7e22e55a", "_filesize": 2929855, "_sha256": "cef74a9d60092197dbfae4a34c83c1aa235b364163c15e721c7a594a7e22e55a", "_created": "2026-05-28T07:02:16.000Z", "_published": "2026-05-28T07:15:46.592Z", "_distro": "noble", "_jobs": [ { "job": 78240363132, "time": 277, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7259716922" }, { "job": 78240363192, "time": 279, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7259717641" }, { "job": 78240363154, "time": 237, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7259833838" }, { "job": 78240363065, "time": 202, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7259814058" }, { "job": 78239614392, "time": 339, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259644669" }, { "job": 78240363036, "time": 195, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259695110" }, { "job": 78240363193, "time": 207, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7259698180" }, { "job": 78240363174, "time": 184, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7259692391" }, { "job": 78240363185, "time": 195, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7259695242" } ], "_buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/saraswatsh/cytoprofile", "_commit": { "id": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "author": "Shubh Saraswat ", "committer": "Shubh Saraswat ", "message": "minor fix to readme\n", "time": 1772214857 }, "_maintainer": { "name": "Shubh Saraswat", "email": "shubh.saraswat00@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3", "role": "Depends" }, { "package": "mixOmics", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "plot3D", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "xgboost", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "e1071", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "spelling", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "Ckmeans.1d.dp", "role": "Suggests" }, { "package": "prodlim", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" } ], "_owner": "saraswatsh", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-31", "n": 1 }, { "week": "2025-32", "n": 1 }, { "week": "2025-33", "n": 2 }, { "week": "2025-35", "n": 2 }, { "week": "2025-36", "n": 3 }, { "week": "2025-49", "n": 4 }, { "week": "2026-02", "n": 3 }, { "week": "2026-09", "n": 2 } ], "_tags": [ { "name": "v0.2.2", "date": "2025-09-04" }, { "name": "v0.2.3", "date": "2025-12-05" }, { "name": "v0.2.4", "date": "2026-02-27" } ], "_stars": 0, "_contributors": [ { "user": "saraswatsh", "count": 131, "uuid": 58528099 } ], "_userbio": { "uuid": 58528099, "type": "user", "name": "Shubh Saraswat", "description": "Biomedical Data Scientist and PhD Student Epidemiology and Biostatistics at University of Kentucky" }, "_downloads": { "count": 284, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CytoProfile" }, "_devurl": "https://github.com/saraswatsh/cytoprofile", "_pkgdown": "https://cytoprofile.cytokineprofile.org/", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/CytoProfile.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/saraswatsh/cytoprofile", "_realowner": "saraswatsh", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2025-04-03" }, { "version": "0.2.0", "date": "2025-04-10" }, { "version": "0.2.1", "date": "2025-05-19" }, { "version": "0.2.2", "date": "2025-09-04" }, { "version": "0.2.3", "date": "2025-12-11" }, { "version": "0.2.4", "date": "2026-02-27" } ], "_exports": [ "adjust_p", "apply_scale", "cyt_anova", "cyt_bp", "cyt_bp2", "cyt_dualflashplot", "cyt_errbp", "cyt_export", "cyt_heatmap", "cyt_mint_splsda", "cyt_pca", "cyt_rf", "cyt_skku", "cyt_splsda", "cyt_ttest", "cyt_univariate", "cyt_univariate_multi", "cyt_violin", "cyt_volc", "cyt_xgb" ], "_datasets": [ { "name": "ExampleData1", "title": "Example Cytokine Profiling Data 1.", "object": "ExampleData1", "class": [ "data.frame" ], "fields": [ "Group", "Treatment", "Time", "IL-17F", "GM-CSF", "IFN-G", "IL-10", "CCL-20/MIP-3A", "IL-12/P70", "IL-13", "IL-15", "IL-17A", "IL-22", "IL-9", "IL-1B", "IL-33", "IL-2", "IL-21", "IL-4", "IL-23", "IL-5", "IL-6", "IL-17E/IL-25", "IL-27", "IL-31", "TNF-A", "TNF-B", "IL-28A" ], "rows": 297, "table": true, "tojson": true }, { "name": "ExampleData2", "title": "Example Cytokine Profiling Data 2.", "object": "ExampleData2", "class": [ "data.frame" ], "fields": [ "Stimulation", "Group", "IL-17F", "GM-CSF", "IFN-G", "IL-10", "CCL-20", "IL-12", "IL-13", "IL-17A", "IL-22", "IL-9", "IL-1B", "IL-2", "IL-21", "IL-4", "IL-5", "IL-6", "TNF-A", "TNF-B" ], "rows": 66, "table": true, "tojson": true }, { "name": "ExampleData3", "title": "Example Cytokine Profiling Data 3.", "object": "ExampleData3", "class": [ "data.frame" ], "fields": [ "Stimulation", "Group", "GM-CSF", "IFN-G", "IL-10", "CCL-20/MIP-3A", "IL-12/P70", "IL-13", "IL-15", "IL-9", "IL-1B", "IL-21", "IL-6", "TNF-A" ], "rows": 64, "table": true, "tojson": true }, { "name": "ExampleData4", "title": "Example Cytokine Profiling Data 4.", "object": "ExampleData4", "class": [ "data.frame" ], "fields": [ "Group", "Treatment", "IL-17F", "GM-CSF", "IFN-G", "IL-10", "CCL-20", "IL-12", "IL-13", "IL-17A", "IL-22", "IL-9", "IL-2", "IL-21", "IL-4", "IL-23", "IL-5", "IL-6", "TNF-A", "TNF-B" ], "rows": 43, "table": true, "tojson": true }, { "name": "ExampleData5", "title": "Example Cytokine Profiling Data 5.", "object": "ExampleData5", "class": [ "data.frame" ], "fields": [ "Group", "Treatment", "Batch", "Time", "IL-17F", "GM-CSF", "IFN-G", "IL-10", "CCL-20/MIP-3A", "IL-12/P70", "IL-13", "IL-15", "IL-17A", "IL-22", "IL-9", "IL-1B", "IL-33", "IL-2", "IL-21", "IL-4", "IL-23", "IL-5", "IL-6", "IL-17E/IL-25", "IL-27", "IL-31", "TNF-A", "TNF-B", "IL-28A" ], "rows": 297, "table": true, "tojson": true } ], "_help": [ { "page": "adjust_p", "title": "Adjust p-values using a specified method", "topics": [ "adjust_p" ] }, { "page": "apply_scale", "title": "Apply a scale transformation to numeric columns", "topics": [ "apply_scale" ] }, { "page": "cyt_anova", "title": "ANOVA Analysis on Continuous Variables. *[Deprecated]*", "topics": [ "cyt_anova" ] }, { "page": "cyt_bp", "title": "Boxplots for Continuous Variables with Optional Grouping", "topics": [ "cyt_bp" ] }, { "page": "cyt_bp2", "title": "Boxplot Function Enhanced for Specific Group Comparisons. *[Deprecated]*", "topics": [ "cyt_bp2" ] }, { "page": "cyt_dualflashplot", "title": "Dual-flashlight Plot", "topics": [ "cyt_dualflashplot" ] }, { "page": "cyt_errbp", "title": "Error-bar Plot", "topics": [ "cyt_errbp" ] }, { "page": "cyt_export", "title": "Generic export function for Cytokine plots", "topics": [ "cyt_export" ] }, { "page": "cyt_heatmap", "title": "Heat Map", "topics": [ "cyt_heatmap" ] }, { "page": "cyt_mint_splsda", "title": "Analyze data with Multivariate INTegration (MINT) Sparse Partial Least Squares Discriminant Analysis (sPLS-DA).", "topics": [ "cyt_mint_splsda" ] }, { "page": "cyt_pca", "title": "Analyze Data with Principal Component Analysis (PCA) for Cytokines.", "topics": [ "cyt_pca" ] }, { "page": "cyt_rf", "title": "Run Random Forest Classification on Cytokine Data,", "topics": [ "cyt_rf" ] }, { "page": "cyt_skku", "title": "Distribution of the Data Set Shown by Skewness and Kurtosis.", "topics": [ "cyt_skku" ] }, { "page": "cyt_splsda", "title": "Analyze data with Sparse Partial Least Squares Discriminant Analysis (sPLS-DA).", "topics": [ "cyt_splsda" ] }, { "page": "cyt_ttest", "title": "Two Sample T-test Comparisons. *[Deprecated]*", "topics": [ "cyt_ttest" ] }, { "page": "cyt_univariate", "title": "Pairwise Univariate Tests Between Two Groups", "topics": [ "cyt_univariate" ] }, { "page": "cyt_univariate_multi", "title": "Univariate Tests for Multi‑Level Categorical Predictors", "topics": [ "cyt_univariate_multi" ] }, { "page": "cyt_violin", "title": "Violin Plots for Continuous Variables with Optional Grouping", "topics": [ "cyt_violin" ] }, { "page": "cyt_volc", "title": "Volcano plot", "topics": [ "cyt_volc" ] }, { "page": "cyt_xgb", "title": "Run XGBoost Classification on Cytokine Data.", "topics": [ "cyt_xgb" ] }, { "page": "ExampleData1", "title": "Example Cytokine Profiling Data 1.", "topics": [ "ExampleData1" ] }, { "page": "ExampleData2", "title": "Example Cytokine Profiling Data 2.", "topics": [ "ExampleData2" ] }, { "page": "ExampleData3", "title": "Example Cytokine Profiling Data 3.", "topics": [ "ExampleData3" ] }, { "page": "ExampleData4", "title": "Example Cytokine Profiling Data 4.", "topics": [ "ExampleData4" ] }, { "page": "ExampleData5", "title": "Example Cytokine Profiling Data 5.", "topics": [ "ExampleData5" ] } ], "_pkglogo": "https://github.com/saraswatsh/cytoprofile/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/saraswatsh/cytoprofile/raw/HEAD/README.md", "_rundeps": [ "base64enc", "BH", "BiocParallel", "bslib", "cachem", "caret", "class", "cli", "clock", "codetools", "corpcor", "cpp11", "data.table", "diagram", "digest", "dplyr", "e1071", "ellipse", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "ggplot2", "ggrepel", "globals", "glue", "gower", "gridExtra", "gtable", "hardhat", "highr", "htmltools", "htmlwidgets", "igraph", "ipred", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "misc3d", "mixOmics", "ModelMetrics", "nlme", "nnet", "numDeriv", "parallelly", "pheatmap", "pillar", "pkgconfig", "plot3D", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "R6", "randomForest", "rappdirs", "rARPACK", "RColorBrewer", "Rcpp", "RcppEigen", "recipes", "reshape2", "rgl", "rlang", "rmarkdown", "rpart", "RSpectra", "S7", "sass", "scales", "shape", "snow", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xgboost", "yaml" ], "_vignettes": [ { "source": "getting_started.Rmd", "filename": "getting_started.html", "title": "Getting Started with CytoProfile", "engine": "knitr::rmarkdown", "headings": [ "Installation and Dependencies", "Required Bioconductor package", "Installing CytoProfile", "Package loading", "1. Data Loading and Format Requirements", "Input data format", "2. Exploratory Data Analysis", "2.1 Boxplots - cyt_bp()", "2.2 Violin Plots - cyt_violin()", "2.3 Skewness and Kurtosis - cyt_skku()", "2.4 Error Bar Plots - cyt_errbp()", "3. Univariate Analysis", "3.1 Two-group comparisons - cyt_univariate()", "3.2 Multi-group comparisons - cyt_univariate_multi()", "4. Statistical Visualizations", "4.1 Volcano Plot - cyt_volc()", "4.2 Heatmap - cyt_heatmap()", "4.3 Dual-Flashlight Plot - cyt_dualflashplot()", "5. Multivariate Analysis", "5.1 Principal Component Analysis - cyt_pca()", "5.2 Sparse PLS-DA - cyt_splsda()", "5.3 MINT sPLS-DA - cyt_mint_splsda()", "6. Machine Learning Models", "6.1 XGBoost Classification - cyt_xgb()", "6.2 Random Forest Classification - cyt_rf()", "7. Saving Plots and Exporting Results", "Saving plots from individual functions", "Saving plots from multivariate functions using cyt_export()", "Modifying returned plots", "8. Recommended Analysis Workflow", "Session Information" ], "created": "2025-03-05 17:27:29", "modified": "2026-02-27 17:23:15", "commits": 22 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "cytoprofile", "_universes": [ "saraswatsh" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.4", "date": "2026-05-28T07:06:08.000Z", "distro": "noble", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "4853179a86f86575e58418d83e2add39ae4a2f086c7c8a2e44f14c00088e5537", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.6.0", "os": "linux", "version": "0.2.4", "date": "2026-05-28T07:06:00.000Z", "distro": "noble", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "c7322a3622aa44477ac42042b3687a8557f746e9094aa75c8e142b731fcb6a64", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.5.3", "os": "mac", "version": "0.2.4", "date": "2026-05-28T07:13:56.000Z", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "f8a77adf9bd1410c91ab54bc02c01ceb5f20c499a955f717470aa70c1ec00e9f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.6.0", "os": "mac", "version": "0.2.4", "date": "2026-05-28T07:12:24.000Z", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "0d8c2d15fe8a92da2d6b2781ba5c957835b2c6e6cfa346c68a011d0ef1b275df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.4", "date": "2026-05-28T07:05:56.000Z", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "0e1c57ff77fef5202d3eb4d73c734a190af14467d5ec62983a05ae2ddd0feb02", "status": "success", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.7.0", "os": "win", "version": "0.2.4", "date": "2026-05-28T07:04:17.000Z", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "0438d287dc11d937020b7aecc44474ab87f9b9a3565deb8f218ffd878fc32983", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.5.3", "os": "win", "version": "0.2.4", "date": "2026-05-28T07:04:18.000Z", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "972274316faf503e553f2a2f5aa002b609ee8a8ba20fcc6362493321913a8eac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" }, { "r": "4.6.0", "os": "win", "version": "0.2.4", "date": "2026-05-28T07:04:26.000Z", "commit": "ba676b9ef0fa79ce42917523ec23dd518e7436e6", "fileid": "30f710dc4a54829da57d4689b28530775bdcb8cf6a4ce6eb113faa35a8d4eb30", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/saraswatsh/actions/runs/26559738547" } ] }