{ "_id": "6a1e7f4e1d7bb097a0a660cb", "Package": "pepdiff", "Type": "Package", "Title": "Differential Abundance Analysis for Phosphoproteomics Data", "Version": "1.0.0", "Author": "Dan MacLean [aut, cre]", "Description": "Provides tools for analyzing differential abundance in\nproteomics experiments. Implements S3 classes for data\nmanagement and supports Generalized Linear Models (GLM; Nelder\nand Wedderburn (1972) ), Aligned Rank\nTransform (ART; Wobbrock et al. (2011)\n), and pairwise test methods for\nstatistical analysis. Includes visualization functions for\nPrincipal Component Analysis (PCA), volcano plots, and\nheatmaps.", "Authors@R": "person(given = \"Dan\", family = \"MacLean\", role = c(\"aut\", \"cre\"), email = \"dan.maclean@tsl.ac.uk\")", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "biocViews": "", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 06:55:14 UTC", "User": "root" }, "Maintainer": "Dan MacLean ", "Config/pak/sysreqs": "cmake make libicu-dev libx11-dev", "Repository": "https://tsl-zz.r-universe.dev", "Date/Publication": "2026-04-02 21:55:23 UTC", "RemoteUrl": "https://github.com/cran/pepdiff", "RemoteRef": "HEAD", "RemoteSha": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "MD5sum": "4ee20220ade3826d9fec17ecb3df0ccb", "_user": "tsl-zz", "_type": "src", "_file": "pepdiff_1.0.0.tar.gz", "_fileid": "bbb7e297b44c10e0342fb77fd4ec56941a26aa2b93409e56dae42b8c7368a485", "_filesize": 2630860, "_sha256": "bbb7e297b44c10e0342fb77fd4ec56941a26aa2b93409e56dae42b8c7368a485", "_created": "2026-06-02T06:55:14.000Z", "_published": "2026-06-02T06:59:26.386Z", "_distro": "noble", "_jobs": [ { "job": 79016078745, "time": 209, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7350993309" }, { "job": 79016078740, "time": 221, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7350996596" }, { "job": 79016078724, "time": 220, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7350988409" }, { "job": 79016078748, "time": 148, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7350971625" }, { "job": 79015567563, "time": 231, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7350936114" }, { "job": 79016078709, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7350978097" }, { "job": 79016078750, "time": 165, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7350981500" }, { "job": 79016078734, "time": 142, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7350975354" }, { "job": 79016078744, "time": 131, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7350972104" } ], "_buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/pepdiff", "_commit": { "id": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "author": "Dan MacLean ", "committer": "cran-robot ", "message": "version 1.0.0\n", "time": 1775166923 }, "_maintainer": { "name": "Dan MacLean", "email": "dan.maclean@tsl.ac.uk", "login": "tsl-zz", "description": "", "uuid": 204196 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "emmeans", "role": "Imports" }, { "package": "ARTool", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "forcats", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Suggests" }, { "package": "UpSetR", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "factoextra", "role": "Suggests" }, { "package": "RankProd", "role": "Suggests" }, { "package": "MKinfer", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 1 } ], "_tags": [ { "name": "1.0.0", "date": "2026-04-02" } ], "_stars": 0, "_contributors": [ { "user": "tsl-zz", "count": 1, "uuid": 204196 } ], "_userbio": { "uuid": 204196, "type": "user", "name": "tsl-zz" }, "_downloads": { "count": 161, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pepdiff" }, "_searchresults": 25, "_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/pepdiff.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "tsl-zz", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2026-04-02" } ], "_exports": [ "%>%", "assess_missing", "classify_bf_evidence", "combine_tech_reps", "compare", "compare_calls", "compare_many", "estimate_result_clusters", "fc_qqplot", "get_bootstrap_percentile", "get_comparison", "get_kruskal_percentile", "get_peptide", "get_rp_percentile", "get_wilcoxon_percentile", "import_data", "kmeans_by_selected_cols", "long_results", "missing_peptides_plot", "norm_qqplot", "p_value_hist", "plot_bf_distribution", "plot_distributions_simple", "plot_fc", "plot_fc_distribution_new", "plot_fit_diagnostics", "plot_heatmap", "plot_kmeans", "plot_missingness_simple", "plot_pca", "plot_pca_simple", "plot_pvalue_histogram", "plot_quant_distributions", "plot_result", "plot_volcano_bf", "plot_volcano_new", "read_pepdiff", "significant", "test_bayes_t", "test_bootstrap_t", "test_rankprod", "test_wilcoxon", "times_measured", "times_measured_plot", "volcano_plot" ], "_help": [ { "page": "assess_missing", "title": "calculate the proportion of peptides with missing values per group in a data set.", "topics": [ "assess_missing" ] }, { "page": "classify_bf_evidence", "title": "Classify Bayes factor into evidence categories", "topics": [ "classify_bf_evidence" ] }, { "page": "combine_tech_reps", "title": "Combine technical replicates", "topics": [ "combine_tech_reps" ] }, { "page": "compare", "title": "Compare peptide abundances between conditions", "topics": [ "compare", "compare.pepdiff_data" ] }, { "page": "compare_calls", "title": "compare sets of significant peptides called by the used data", "topics": [ "compare_calls" ] }, { "page": "compare_many", "title": "compare many combinations of treatment and control", "topics": [ "compare_many" ] }, { "page": "compare.data.frame", "title": "Default compare method for legacy data frames", "topics": [ "compare.data.frame" ] }, { "page": "estimate_result_clusters", "title": "plots a Figure of Merit curve to help estimate the number of clusters in the results", "topics": [ "estimate_result_clusters" ] }, { "page": "fc_qqplot", "title": "plot qqplot of fold changes from a comparison", "topics": [ "fc_qqplot" ] }, { "page": "fold_change_matrix", "title": "returns a matrix of fold change values", "topics": [ "fold_change_matrix" ] }, { "page": "get_bootstrap_percentile", "title": "get p values for contrast using boostrap t test", "topics": [ "get_bootstrap_percentile" ] }, { "page": "get_comparison", "title": "Get results for a specific comparison", "topics": [ "get_comparison" ] }, { "page": "get_kruskal_percentile", "title": "get p values for contrast using Kruskal-Wallis test", "topics": [ "get_kruskal_percentile" ] }, { "page": "get_peptide", "title": "Get results for a specific peptide", "topics": [ "get_peptide" ] }, { "page": "get_rp_percentile", "title": "get p values for contrast using Rank Products test", "topics": [ "get_rp_percentile" ] }, { "page": "get_sig_rows", "title": "works out if a peptide has at least one significant value across the experiment Composes a matrix of the `metric` significance values with peptides in rows, experiments in columns and works out if each peptide row has a value below the stated cut off", "topics": [ "get_sig_rows" ] }, { "page": "get_wilcoxon_percentile", "title": "get p values for contrast using Wilcoxon test", "topics": [ "get_wilcoxon_percentile" ] }, { "page": "import_data", "title": "read data from a file", "topics": [ "import_data" ] }, { "page": "kmeans_by_selected_cols", "title": "Perform kmeans of a dataset using just data in selected columns, then return matrices of all columns", "topics": [ "kmeans_by_selected_cols" ] }, { "page": "list2mat", "title": "converts a results object to a matrix as if for direct use in external heatmap functions", "topics": [ "list2mat" ] }, { "page": "long_results", "title": "Convert wide format results table to long format", "topics": [ "long_results" ] }, { "page": "metrics", "title": "reports metrics available for significance values", "topics": [ "metrics" ] }, { "page": "missing_peptides_plot", "title": "plot the representation of peptides in each group.", "topics": [ "missing_peptides_plot" ] }, { "page": "norm_qqplot", "title": "draw qqplots for data", "topics": [ "norm_qqplot" ] }, { "page": "p_value_hist", "title": "plot histograms of p-values for each test used", "topics": [ "p_value_hist" ] }, { "page": "plot_bf_distribution", "title": "Bayes factor distribution plot", "topics": [ "plot_bf_distribution" ] }, { "page": "plot_distributions_simple", "title": "Simple distribution plot for pepdiff_data", "topics": [ "plot_distributions_simple" ] }, { "page": "plot_fc", "title": "plot histogram of fold change distribution for a comparison", "topics": [ "plot_fc" ] }, { "page": "plot_fc_distribution_new", "title": "Fold change distribution for pepdiff_results", "topics": [ "plot_fc_distribution_new" ] }, { "page": "plot_fit_diagnostics", "title": "Plot GLM fit diagnostics", "topics": [ "plot_fit_diagnostics" ] }, { "page": "plot_heatmap", "title": "makes heatmap from all experiments, filter on a single metric and sig value", "topics": [ "plot_heatmap" ] }, { "page": "plot_kmeans", "title": "K-means cluster the data on the samples", "topics": [ "plot_kmeans" ] }, { "page": "plot_missingness_simple", "title": "Simple missingness plot for pepdiff_data", "topics": [ "plot_missingness_simple" ] }, { "page": "plot_pca", "title": "plots a pca on the treatment, seconds, bio-rep", "topics": [ "plot_pca" ] }, { "page": "plot_pca_simple", "title": "Simple PCA plot for pepdiff_data", "topics": [ "plot_pca_simple" ] }, { "page": "plot_pvalue_histogram", "title": "P-value histogram for pepdiff_results", "topics": [ "plot_pvalue_histogram" ] }, { "page": "plot_quant_distributions", "title": "draw density plots for data", "topics": [ "plot_quant_distributions" ] }, { "page": "plot_result", "title": "plot the p-values against fold change for the tests used in `compare()`", "topics": [ "plot_result" ] }, { "page": "plot_volcano_bf", "title": "Volcano plot for Bayes factor results", "topics": [ "plot_volcano_bf" ] }, { "page": "plot_volcano_new", "title": "Volcano plot for pepdiff_results", "topics": [ "plot_volcano_new" ] }, { "page": "plot.pepdiff_data", "title": "Plot method for pepdiff_data", "topics": [ "plot.pepdiff_data" ] }, { "page": "plot.pepdiff_results", "title": "Plot method for pepdiff_results", "topics": [ "plot.pepdiff_results" ] }, { "page": "print.pepdiff_data", "title": "Print method for pepdiff_data", "topics": [ "print.pepdiff_data" ] }, { "page": "print.pepdiff_results", "title": "Print method for pepdiff_results", "topics": [ "print.pepdiff_results" ] }, { "page": "read_pepdiff", "title": "Read proteomics data into a pepdiff_data object", "topics": [ "read_pepdiff" ] }, { "page": "significant", "title": "Extract significant results", "topics": [ "significant" ] }, { "page": "subset.pepdiff_data", "title": "Subset a pepdiff_data object", "topics": [ "subset.pepdiff_data" ] }, { "page": "summary.pepdiff_data", "title": "Summary method for pepdiff_data", "topics": [ "summary.pepdiff_data" ] }, { "page": "summary.pepdiff_results", "title": "Summary method for pepdiff_results", "topics": [ "summary.pepdiff_results" ] }, { "page": "test_bayes_t", "title": "Bayes factor t-test for two groups", "topics": [ "test_bayes_t" ] }, { "page": "test_bootstrap_t", "title": "Bootstrap t-test for two groups", "topics": [ "test_bootstrap_t" ] }, { "page": "test_rankprod", "title": "Rank products test for two groups", "topics": [ "test_rankprod" ] }, { "page": "test_wilcoxon", "title": "Wilcoxon rank-sum test for two groups", "topics": [ "test_wilcoxon" ] }, { "page": "times_measured", "title": "calculate number of measurements of each peptide in each treatment and time", "topics": [ "times_measured" ] }, { "page": "times_measured_plot", "title": "plot the count of the number of times peptides were measured.", "topics": [ "times_measured_plot" ] }, { "page": "volcano_plot", "title": "volcano plot the data", "topics": [ "volcano_plot" ] } ], "_pkglogo": "https://github.com/cran/pepdiff/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/cran/pepdiff/raw/HEAD/README.md", "_rundeps": [ "abind", "ARTool", "backports", "bit", "bit64", "boot", "broom", "car", "carData", "cli", "clipr", "colorspace", "cowplot", "cpp11", "crayon", "Deriv", "doBy", "dplyr", "emmeans", "estimability", "farver", "forcats", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "glue", "gtable", "hms", "isoband", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "microbenchmark", "minqa", "modelr", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "plyr", "prettyunits", "progress", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "readr", "reformulas", "rlang", "S7", "scales", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tzdb", "urca", "utf8", "vctrs", "viridisLite", "vroom", "withr", "zoo" ], "_vignettes": [ { "source": "checking_fit.Rmd", "filename": "checking_fit.html", "title": "Checking GLM Model Fit", "engine": "knitr::rmarkdown", "headings": [ "Why Check Model Fit?", "Quick Check with plot_fit_diagnostics()", "Reading the Diagnostic Plots", "Panel A: Deviance Distribution", "Panel B: Deviance vs Effect Size", "Panel C: Sample Residual Plots", "Panel D: Pooled QQ Plot", "Investigating Flagged Peptides", "Example: Data with Poor Fit", "Decision: GLM or ART?", "Use GLM when:", "Consider ART when:", "Try ART on the problematic data:", "Summary" ], "created": "2026-04-02 21:55:23", "modified": "2026-04-02 21:55:23", "commits": 1 }, { "source": "glm_analysis.Rmd", "filename": "glm_analysis.html", "title": "Factorial Designs with GLM", "engine": "knitr::rmarkdown", "headings": [ "When you need GLM", "Why Gamma GLM?", "Example: 2×2 factorial design", "The simulated peptide groups", "What these patterns look like in raw data", "Basic GLM analysis: main effects", "Did GLM find the treatment effects?", "Stratified comparisons with within", "Stratified results by group", "Handling interactions", "When to use main effects vs stratified", "Checking convergence", "Model checking", "Exporting results", "Practical recommendations", "Quick interaction check", "When GLM struggles" ], "created": "2026-04-02 21:55:23", "modified": "2026-04-02 21:55:23", "commits": 1 }, { "source": "basic_workflow.Rmd", "filename": "basic_workflow.html", "title": "Getting Started with pepdiff", "engine": "knitr::rmarkdown", "headings": [ "What is pepdiff?", "Installation", "Setup", "Creating example data", "Importing data", "Quick look at your data", "Running a comparison", "Understanding results", "Getting significant hits", "Visualising results", "Comparing with our simulation", "Next steps" ], "created": "2026-04-02 21:55:23", "modified": "2026-04-02 21:55:23", "commits": 1 }, { "source": "art_analysis.Rmd", "filename": "art_analysis.html", "title": "Non-parametric Factorial Analysis with ART", "engine": "knitr::rmarkdown", "headings": [ "What is ART?", "When to consider ART", "Example: 2×2 factorial design", "The simulated peptide groups", "What these patterns look like in raw data", "Running ART analysis", "Did ART find the treatment effects?", "Stratified comparisons with within", "Stratified results by group", "Handling interactions", "ART vs GLM comparison", "Diagnostics", "Exporting results", "Limitations of ART", "Practical recommendations", "When both methods fail" ], "created": "2026-04-02 21:55:23", "modified": "2026-04-02 21:55:23", "commits": 1 }, { "source": "pairwise_tests.Rmd", "filename": "pairwise_tests.html", "title": "Two-Group Comparisons with Pairwise Tests", "engine": "knitr::rmarkdown", "headings": [ "When to use pairwise tests", "Example data", "The four pairwise tests", "Wilcoxon rank-sum test", "Bootstrap t-test", "Bayes factor t-test", "Rank products", "How Rank Products differs from other tests", "Comparing results across tests", "FDR correction (p-value tests only)", "Visualising results", "Bayes factor plots", "When pairwise isn't enough" ], "created": "2026-04-02 21:55:23", "modified": "2026-04-02 21:55:23", "commits": 1 }, { "source": "diagnostic_plots.Rmd", "filename": "diagnostic_plots.html", "title": "Visual Quality Control and Interpretation", "engine": "knitr::rmarkdown", "headings": [ "Why visualise?", "Creating example datasets", "Data-level diagnostics", "PCA plot", "Distribution plots", "Missingness plot", "Results-level diagnostics", "Volcano plot", "P-value histogram", "Fold change distribution", "Individual plot functions", "Exporting for publication", "Summary: what to check" ], "created": "2026-04-02 21:55:23", "modified": "2026-04-02 21:55:23", "commits": 1 } ], "_score": 3.8750612633917, "_indexed": true, "_nocasepkg": "pepdiff", "_universes": [ "tsl-zz" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-02T06:58:03.000Z", "distro": "noble", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "39bb7d7fa9d8455063b6460de7999900ed5929dbd0adf186842a11679e3cd4f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-02T06:58:07.000Z", "distro": "noble", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "8aa053bbf426a4ab9ef4a93e4132f3ad0be33c65c4fadeb651187f79f8780a37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-02T06:57:59.000Z", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "02eacd74ba4e7444894fa42e1feb4917a78f6b9bf09083ec296ce1155b1c57c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-02T06:57:04.000Z", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "7fc74e2e8a0a2c3a3ec29ced942bdd75db0511f7b95b801c2948d5f01330af45", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-02T06:58:01.000Z", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "9925c5e7c7b1e6d1315535dcd326f07cdf7231b1ea076daaa0ef42e55ed32ac8", "status": "success", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-06-02T06:57:00.000Z", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "0d6fe9faa8f8c825ea888957197b2005f5cb14201a0dc8e1029ddc36e83f26d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-06-02T06:56:44.000Z", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "0c9600b91846ffb2d900498a47e6bd10f86e155288c416b185c85b606ef6b277", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-06-02T06:56:35.000Z", "commit": "f6eca2d6d2d03f4de22082e3eaa0da030447f14a", "fileid": "ed32602a32c45bc8af045767ee8dc3c187c9ddfe04c0f8d077b099e05facc319", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tsl-zz/actions/runs/26803559474" } ] }