{ "_id": "6a60f0391fed6d528131bdd7", "Package": "MRManalyzeR", "Type": "Package", "Title": "Process and Analyse Targeted LC-MS Lipidomics and Metabolomics\nData", "Version": "0.99.0", "Authors@R": "person(\"Matthew J.\", \"Smith\",\nemail = \"mattyjsmith123@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7357-2670\"))", "Description": "Reproducible post-acquisition processing of targeted\nLC-MS/MS lipidomics and metabolomics results exported from\nWaters TargetLynx or from Skyline, or supplied as a plain\nsample-by-analyte matrix. Reads the quantitative result tables,\nintegrates them with sample and feature metadata, and applies\nconfigurable signal filtering (SNR, LOD or LOQ), blank\nfiltering, normalisation, internal-standard and volume\nadjustment of vendor-reported concentrations, missing-value\nimputation and batch correction. Each step is an exported\nfunction acting on a struct DatasetExperiment; a complete\nworkflow can additionally be driven from a single YAML\nconfiguration via run_MRManalyzeR(), which also renders\nself-contained HTML data-quality and statistical reports.\nChromatographic peak detection, peak integration and\ncalibration-curve fitting from raw mass-spectrometry data are\noutside its scope.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Metabolomics, Lipidomics, MassSpectrometry, QualityControl,\nNormalization, BatchEffect, Visualization, WorkflowStep", "URL": "https://github.com/MJS-708/MRManalyzeR", "BugReports": "https://github.com/MJS-708/MRManalyzeR/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-07-22 15:53:00 UTC", "RemoteUrl": "https://github.com/BiocStaging/MRManalyzeR", "RemoteRef": "HEAD", "RemoteSha": "5e00a87a8b3e948c3998aa23953087eefd06e632", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-22 16:13:35 UTC", "User": "root" }, "Author": "Matthew J. Smith [aut, cre] (ORCID:\n)", "Maintainer": "Matthew J. Smith ", "_user": "biocstaging", "_type": "src", "_file": "MRManalyzeR_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/e128f0cc42c7313506140a40faf5d12f85459c640b729b384e9faf4873c6660b", "_filesize": 2670997, "_sha256": "e128f0cc42c7313506140a40faf5d12f85459c640b729b384e9faf4873c6660b", "_expires": "2026-10-30T16:30:47.000Z", "_created": "2026-07-22T16:13:35.000Z", "_published": "2026-07-22T16:30:49.471Z", "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953", "_status": "success", "_upstream": "https://github.com/BiocStaging/MRManalyzeR", "_commit": { "id": "5e00a87a8b3e948c3998aa23953087eefd06e632", "author": "Matthew Smith ", "committer": "Matthew Smith ", "message": "Merge branch 'dev'\n", "time": 1784735580 }, "_maintainer": { "name": "Matthew J. Smith", "email": "mattyjsmith123@gmail.com", "login": "mjs-708", "orcid": "0000-0002-7357-2670", "description": "", "uuid": 35523649 }, "_distro": "resolute", "_jobs": [ { "job": 88981350319, "time": 192, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8536664648" }, { "job": 88981350365, "time": 288, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8536714753" }, { "job": 88981350345, "time": 285, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8536713597" }, { "job": 88981350430, "time": 193, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8536664767" }, { "job": 88981350527, "time": 222, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8536680313" }, { "job": 88980056963, "time": 298, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8536563304" }, { "job": 88981350266, "time": 960, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8537052373" }, { "job": 88981350421, "time": 236, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8536687601" }, { "job": 88981350405, "time": 238, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8536688396" }, { "job": 88981350367, "time": 249, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8536694166" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "struct", "role": "Depends" }, { "package": "magrittr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "yaml", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "janitor", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-18", "n": 1 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 1 }, { "week": "2026-30", "n": 2 } ], "_tags": [], "_topics": [ "metabolomics", "lipidomics", "massspectrometry", "qualitycontrol", "normalization", "batcheffect", "visualization", "workflowstep" ], "_stars": 0, "_contributors": [ { "user": "mjs-708", "count": 2, "uuid": 35523649 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 1 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MRManalyzeR" }, "_devurl": "https://github.com/mjs-708/mrmanalyzer", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MRManalyzeR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_cv_metrics", "adjust_concentration", "assemble_dataset", "combine_datasets", "correct_batch", "filter_blanks", "impute_missing", "load_config", "load_dataset", "normalise_matrix", "plot_boxplot", "plot_correlation", "plot_drift", "plot_heatmap", "plot_loadings", "plot_pca", "plot_qq", "plot_volcano", "process_dataset", "read_peak_matrix", "read_skyline", "read_targetlynx", "run_example", "run_MRManalyzeR", "run_MRManalyzeR_combine", "run_pca", "run_stats", "subset_dataset", "summarise_features", "summarise_groups", "validate_config", "validate_design", "validate_input" ], "_help": [ { "page": "add_cv_metrics", "title": "Add per-compound CV metrics to a dataset", "concept": [ "QC check" ], "topics": [ "add_cv_metrics" ] }, { "page": "adjust_concentration", "title": "Adjust a dataset to true sample concentrations", "concept": [ "peak-matrix processing" ], "topics": [ "adjust_concentration" ] }, { "page": "assemble_dataset", "title": "Assemble a struct::DatasetExperiment from a matrix + metadata", "concept": [ "data parse" ], "topics": [ "assemble_dataset" ] }, { "page": "combine_datasets", "title": "Combine multiple processed datasets into one", "concept": [ "data parse" ], "topics": [ "combine_datasets" ] }, { "page": "correct_batch", "title": "Batch-correct a DatasetExperiment (median-ratio)", "concept": [ "peak-matrix processing" ], "topics": [ "correct_batch" ] }, { "page": "filter_blanks", "title": "Blank-filter a dataset (mask values at or below the blank level)", "concept": [ "peak-matrix processing" ], "topics": [ "filter_blanks" ] }, { "page": "impute_missing", "title": "Impute missing values with a fraction of the per-feature minimum", "concept": [ "peak-matrix processing" ], "topics": [ "impute_missing" ] }, { "page": "load_config", "title": "Load a project YAML, resolving !concat_path and !concat_str anchors", "concept": [ "data parse" ], "topics": [ "load_config" ] }, { "page": "load_dataset", "title": "Load a `DatasetExperiment` from `.RDS` or `.xlsx`", "concept": [ "data parse" ], "topics": [ "load_dataset" ] }, { "page": "normalise_matrix", "title": "Normalise a dataset by a per-sample metadata column", "concept": [ "peak-matrix processing" ], "topics": [ "normalise_matrix" ] }, { "page": "plot_boxplot", "title": "Per-compound box or bar plot by group", "concept": [ "stats" ], "topics": [ "plot_boxplot" ] }, { "page": "plot_correlation", "title": "Feature-by-feature correlation heatmap", "concept": [ "stats" ], "topics": [ "plot_correlation" ] }, { "page": "plot_drift", "title": "Plot one compound's intensity against injection order", "concept": [ "QC check" ], "topics": [ "plot_drift" ] }, { "page": "plot_heatmap", "title": "Sample-by-feature heatmap with class annotations", "concept": [ "stats" ], "topics": [ "plot_heatmap" ] }, { "page": "plot_loadings", "title": "Plot PCA loadings as ranked bars, one panel per component", "concept": [ "QC check" ], "topics": [ "plot_loadings" ] }, { "page": "plot_pca", "title": "Plot PCA scores, coloured by a sample-metadata column", "concept": [ "QC check" ], "topics": [ "plot_pca" ] }, { "page": "plot_qq", "title": "Normal Q-Q plot for one compound", "concept": [ "QC check" ], "topics": [ "plot_qq" ] }, { "page": "plot_volcano", "title": "Volcano plot for one comparison", "concept": [ "stats" ], "topics": [ "plot_volcano" ] }, { "page": "print.mrm_validation", "title": "Print a validation result", "topics": [ "print.mrm_validation" ] }, { "page": "process_dataset", "title": "Build a sample x compound matrix from TargetLynx or Skyline input", "concept": [ "peak-matrix processing" ], "topics": [ "process_dataset" ] }, { "page": "read_peak_matrix", "title": "Read a plain sample x compound matrix", "concept": [ "data parse" ], "topics": [ "read_peak_matrix" ] }, { "page": "read_skyline", "title": "Read Skyline sheet(s) into a wide sample x compound matrix", "concept": [ "data parse" ], "topics": [ "read_skyline" ] }, { "page": "read_targetlynx", "title": "Read a TargetLynx workbook into a wide sample x compound matrix", "concept": [ "data parse" ], "topics": [ "read_targetlynx" ] }, { "page": "run_example", "title": "Render the bundled example MRManalyzeR reports", "concept": [ "entry points" ], "topics": [ "run_example" ] }, { "page": "run_MRManalyzeR", "title": "Run the post-acquisition MRManalyzeR workflow from a YAML config", "concept": [ "entry points" ], "topics": [ "run_MRManalyzeR" ] }, { "page": "run_MRManalyzeR_combine", "title": "Run the combine-mode workflow from a dedicated combine YAML", "concept": [ "entry points" ], "topics": [ "run_MRManalyzeR_combine" ] }, { "page": "run_pca", "title": "Pre-process a sample x feature matrix and run PCA", "concept": [ "QC check" ], "topics": [ "run_pca" ] }, { "page": "run_stats", "title": "Run all statistics defined by the YAML `stats_report:` block", "concept": [ "stats" ], "topics": [ "run_stats" ] }, { "page": "subset_dataset", "title": "Subset a `DatasetExperiment` by sample-metadata conditions", "concept": [ "peak-matrix processing" ], "topics": [ "subset_dataset" ] }, { "page": "summarise_features", "title": "Summarise which compounds were reported and which were dropped", "concept": [ "QC check" ], "topics": [ "summarise_features" ] }, { "page": "summarise_groups", "title": "Per-group summary statistics for every compound", "concept": [ "stats" ], "topics": [ "summarise_groups" ] }, { "page": "validate_config", "title": "Validate a YAML configuration", "concept": [ "data parse" ], "topics": [ "validate_config" ] }, { "page": "validate_design", "title": "Validate a study design against the data", "concept": [ "data parse" ], "topics": [ "validate_design" ] }, { "page": "validate_input", "title": "Validate a workbook before processing it", "concept": [ "data parse" ], "topics": [ "validate_input" ] } ], "_readme": "https://github.com/BiocStaging/MRManalyzeR/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "Biobase", "BiocGenerics", "bslib", "cachem", "cli", "cpp11", "curl", "DelayedArray", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "hms", "htmltools", "httr2", "IRanges", "isoband", "janitor", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "lubridate", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "openxlsx", "pheatmap", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snakecase", "SparseArray", "stringi", "stringr", "struct", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml", "zip" ], "_vignettes": [ { "source": "MRManalyzeR.Rmd", "filename": "MRManalyzeR.html", "title": "Processing targeted LC-MS/MS lipidomics and metabolomics with MRManalyzeR", "author": "Matthew J. Smith", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Scope, and where this sits among related packages", "Assumptions and limitations", "How the package is organised", "Installation", "Quick start", "Stage 1: data parse", "The curated workbook", "The TargetLynx export", "The simulated dataset used from here on", "Assembling a DatasetExperiment", "Stage 2: peak-matrix processing", "Blank filter", "Normalise", "Concentration adjustment", "Impute missing values", "Batch correction", "The whole matrix in one call", "Stage 3: QC check", "How well was each compound measured?", "Analytical drift", "Normality", "PCA", "Loadings", "What was reported, and what was dropped", "Stage 4: statistics", "Selecting the biological samples", "Group summaries", "Comparisons", "Per-compound plots", "Volcano", "Heatmap", "Feature correlations", "Ion ratios", "Driving it from a YAML config", "Merging several acquisition panels", "References", "Session info" ], "created": "2026-07-22 15:40:34", "modified": "2026-07-22 15:40:34", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "mrmanalyzer", "_universes": [ "biocstaging", "mjs-708" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-07-22T16:16:35.000Z", "distro": "resolute", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/53c40cbc2cfdc1ae32104e0d2b9e86657a4de3a2de89abeae0c84f6df61bf3e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.6.1", "os": "linux", "version": "0.99.0", "date": "2026-07-22T16:16:36.000Z", "distro": "resolute", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/16975f7701bcfd7af271c75db2a98bdae8b1044281dd462b57849a697d107c08", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-07-22T16:15:44.000Z", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/4d6794142d0d57a9f34fbe601dc77fd085c74f15f719d76577aa575cd67193bc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.6.1", "os": "mac", "version": "0.99.0", "date": "2026-07-22T16:15:44.000Z", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/1f839f503baee44fe27098060323a9062804ba3a54ae838c019fb599273648a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-07-22T16:30:14.000Z", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/048defcb66d319e50e80d825e3740b4c80fe2b4e76d6d3cc87cfb7a93b58d371", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-07-22T16:15:36.000Z", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/a6f6ea5e963454195057ea678f48e4bc7cc94e9d92fc46ad24731cd7d6e861c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-07-22T16:15:59.000Z", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/69bfda1c27e0fab9662f9c9847ce4268ea58236c776a30eab4cdadfa55ef137e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" }, { "r": "4.6.1", "os": "win", "version": "0.99.0", "date": "2026-07-22T16:16:03.000Z", "commit": "5e00a87a8b3e948c3998aa23953087eefd06e632", "fileid": "https://r2.ropensci.org/ca0659c0b87127d85c8e23d4030d75f9cfdd5f132b1dc1112ce9d21aac92f7e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/29936690953" } ] }