{ "_id": "6a626523d3420cf5dfdb3a0f", "Package": "quantMSImageR", "Title": "Processing and Quantification of Targeted Mass Spectrometry\nImaging Data", "Version": "0.99.0", "Authors@R": "person(\"Matthew J.\", \"Smith\", , \"mattyjsmith123@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7357-2670\"))", "Description": "Implements tools for processing and quantifying targeted\nDESI-MRM mass spectrometry imaging (MSI) datasets, extending\nthe Cardinal package. Includes signal-to-noise filtering\nagainst background pixels, tissue/background separation,\nper-feature ion images, quantile heatmaps, quantification\nagainst on-slide or on-tissue calibration standards, and batch\nexport of per-feature text images for external viewers.", "License": "MIT + file LICENSE", "URL": "https://mjs-708.github.io/quantMSImageR,\nhttps://github.com/MJS-708/quantMSImageR", "BugReports": "https://github.com/MJS-708/quantMSImageR/issues", "biocViews": "Software, MassSpectrometry, ImagingMassSpectrometry,\nMetabolomics, Lipidomics, QualityControl, Normalization,\nVisualization", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Collate": "'setClasses.R' 'accessors.R' 'align_features.R' 'applySNR.R'\n'back2NA.R' 'bind_panels.R' 'build_feature_meta.R'\n'combine_MSIs.R' 'createMSIDatamatrix.R' 'create_cal_curve.R'\n'generate_txt_images.R' 'imageR.R' 'int2conc.R'\n'int2response.R' 'int2snr.R' 'join_ion_library.R' 'palettes.R'\n'plot_cal_coverage.R' 'quantMSImageR-package.R' 'quantile_hm.R'\n'read_mrm.R' 'remove_blank_mzs.R' 'run_example.R' 'run_study.R'\n'select_tissue_pixels.R' 'summarise_cal_levels.R' 'trim_MSI.R'\n'validate.R' 'zero2na.R'", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev perl", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-07-23 17:04:48 UTC", "RemoteUrl": "https://github.com/BiocStaging/quantMSImageR", "RemoteRef": "HEAD", "RemoteSha": "8be881d9e298069154b9d4bf39caf59e68d27c08", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-23 18:56:29 UTC", "User": "root" }, "Author": "Matthew J. Smith [aut, cre] (ORCID:\n)", "Maintainer": "Matthew J. Smith ", "_user": "biocstaging", "_type": "src", "_file": "quantMSImageR_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/7440b3ba3cb6eac75b9876f115c7ab1e7233b9c227e48dcb6a185eaa117a6d9c", "_filesize": 1750534, "_sha256": "7440b3ba3cb6eac75b9876f115c7ab1e7233b9c227e48dcb6a185eaa117a6d9c", "_expires": "2026-10-31T19:01:53.000Z", "_created": "2026-07-23T18:56:29.000Z", "_published": "2026-07-23T19:01:55.586Z", "_bioccheck": { "error": 0, "warning": 2, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066", "_status": "success", "_upstream": "https://github.com/BiocStaging/quantMSImageR", "_commit": { "id": "8be881d9e298069154b9d4bf39caf59e68d27c08", "author": "Matthew Smith ", "committer": "Matthew Smith ", "message": "Match the package help title to DESCRIPTION\n", "time": 1784826288 }, "_maintainer": { "name": "Matthew J. Smith", "email": "mattyjsmith123@gmail.com", "login": "mjs-708", "orcid": "0000-0002-7357-2670", "description": "", "uuid": 35523649 }, "_distro": "resolute", "_jobs": [ { "job": 89303791023, "time": 200, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8575319774" }, { "job": 89303791149, "time": 271, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8575355025" }, { "job": 89303791150, "time": 265, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8575351623" }, { "job": 89303791009, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8575285820" }, { "job": 89303791050, "time": 193, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8575315345" }, { "job": 89302449677, "time": 327, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8575221960" }, { "job": 89303791184, "time": 169, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8575305165" }, { "job": 89303791131, "time": 198, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8575319445" }, { "job": 89303791139, "time": 212, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "8575326294" }, { "job": 89303791109, "time": 218, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8575328808" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Cardinal", "version": ">= 3.6.2", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "chemCal", "version": ">= 0.2.3", "role": "Imports" }, { "package": "viridis", "version": ">= 0.6.5", "role": "Imports" }, { "package": "ComplexHeatmap", "version": ">= 2.20.0", "role": "Imports" }, { "package": "circlize", "version": ">= 0.4.15", "role": "Imports" }, { "package": "matrixStats", "version": ">= 0.63.0", "role": "Imports" }, { "package": "pracma", "version": ">= 2.4.0", "role": "Imports" }, { "package": "rmarkdown", "version": ">= 2.20", "role": "Imports" }, { "package": "purrr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "CardinalIO", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ProtGenerics", "version": ">= 1.34.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.4", "role": "Imports" }, { "package": "ggplot2", "version": ">= 4.0.0", "role": "Imports" }, { "package": "tibble", "version": ">= 3.2.1", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "patchwork", "version": ">= 1.2.0", "role": "Imports" }, { "package": "yaml", "version": ">= 2.3.0", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.40", "role": "Suggests" }, { "package": "BiocStyle", "version": ">= 2.28.0", "role": "Suggests" }, { "package": "rstudioapi", "version": ">= 0.15.0", "role": "Suggests" }, { "package": "DT", "version": ">= 0.33", "role": "Suggests" }, { "package": "htmltools", "version": ">= 0.5.0", "role": "Suggests" }, { "package": "magick", "version": ">= 2.8.4", "role": "Suggests" }, { "package": "openxlsx", "version": ">= 4.2.0", "role": "Suggests" }, { "package": "matter", "version": ">= 2.0.0", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-18", "n": 2 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 1 }, { "week": "2026-23", "n": 2 }, { "week": "2026-28", "n": 1 }, { "week": "2026-30", "n": 32 } ], "_tags": [], "_topics": [ "software", "massspectrometry", "imagingmassspectrometry", "metabolomics", "lipidomics", "qualitycontrol", "normalization", "visualization" ], "_stars": 0, "_contributors": [ { "user": "mjs-708", "count": 1, "uuid": 35523649 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 1 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/quantMSImageR" }, "_devurl": "https://github.com/mjs-708/quantmsimager", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/quantMSImageR.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "align_features", "applySNR", "back2NA", "bind_panels", "build_feature_meta", "calibrationData", "calibrationData<-", "calibrationDiagnostics", "calibrationInfo", "calibrationLevels", "calibrationMetadata", "calibrationModels", "calibrationModels<-", "calibrationR2", "combine_MSIs", "create_cal_curve", "createMSIDatamatrix", "generate_txt_images", "imageR", "int2conc", "int2response", "int2snr", "plot_cal_coverage", "quant_MSImagingExperiment", "quant_palettes", "quantile_hm", "read_mrm", "remove_blank_mzs", "run_example", "run_study", "select_tissue_pixels", "summarise_cal_levels", "tissueData", "tissueInfo", "tissueMatrix", "trim_MSI", "validate_config", "zero2na" ], "_help": [ { "page": "align_features", "title": "Align two MSI objects to their common features", "concept": [ "combining acquisitions" ], "topics": [ "align_features" ] }, { "page": "applySNR-quant_MSImagingExperiment-method", "title": "Apply SNR mask to intensity values", "concept": [ "filtering" ], "topics": [ "applySNR", "applySNR,quant_MSImagingExperiment-method" ] }, { "page": "back2NA-quant_MSImagingExperiment-method", "title": "Set background pixel intensities to NA", "concept": [ "filtering" ], "topics": [ "back2NA", "back2NA,quant_MSImagingExperiment-method" ] }, { "page": "bind_panels", "title": "Merge two MSI objects of the same tissue by coordinate-matched rbind", "concept": [ "combining acquisitions" ], "topics": [ "bind_panels" ] }, { "page": "build_feature_meta", "title": "Build per-feature metadata by joining an ion library on m/z", "topics": [ "build_feature_meta" ] }, { "page": "calibrationInfo-class", "title": "Calibration metadata for an imaging experiment", "concept": [ "calibration" ], "topics": [ "calibrationInfo", "calibrationInfo-class" ] }, { "page": "combine_MSIs-MSImagingExperiment-method", "title": "Combine MSI experiments across acquisitions", "concept": [ "combining acquisitions" ], "topics": [ "combine_MSIs", "combine_MSIs,MSImagingExperiment-method" ] }, { "page": "create_cal_curve-quant_MSImagingExperiment-method", "title": "Fit per-analyte calibration models", "concept": [ "calibration" ], "topics": [ "create_cal_curve", "create_cal_curve,quant_MSImagingExperiment-method" ] }, { "page": "createMSIDatamatrix-quant_MSImagingExperiment-method", "title": "Create a feature-by-sample MSI data matrix", "topics": [ "createMSIDatamatrix", "createMSIDatamatrix,quant_MSImagingExperiment-method" ] }, { "page": "generate_txt_images", "title": "Load, process and optionally export per-feature text-image matrices", "concept": [ "workflow" ], "topics": [ "generate_txt_images" ] }, { "page": "imageR-quant_MSImagingExperiment-method", "title": "Draw an ion image for one feature", "concept": [ "visualisation" ], "topics": [ "imageR", "imageR,quant_MSImagingExperiment-method" ] }, { "page": "int2conc-quant_MSImagingExperiment-method", "title": "Convert response to calibrated amount estimates", "concept": [ "calibration" ], "topics": [ "int2conc", "int2conc,quant_MSImagingExperiment-method" ] }, { "page": "int2response-quant_MSImagingExperiment-method", "title": "Normalise pixel intensities to internal-standard response", "concept": [ "filtering" ], "topics": [ "int2response", "int2response,quant_MSImagingExperiment-method" ] }, { "page": "int2snr-quant_MSImagingExperiment-method", "title": "Calculate background-referenced signal-to-noise ratios", "concept": [ "filtering" ], "topics": [ "int2snr", "int2snr,quant_MSImagingExperiment-method" ] }, { "page": "plot_cal_coverage-quant_MSImagingExperiment-method", "title": "Check that measured pixels fall within the calibrated range", "concept": [ "calibration" ], "topics": [ "plot_cal_coverage", "plot_cal_coverage,quant_MSImagingExperiment-method" ] }, { "page": "print.quant_validation", "title": "Print a validation result", "concept": [ "workflow" ], "topics": [ "print.quant_validation" ] }, { "page": "quant_MSImagingExperiment", "title": "Quantifiable MS imaging experiment", "topics": [ "quant_MSImagingExperiment", "quant_MSImagingExperiment-class" ] }, { "page": "quant_palettes", "title": "Colour palettes used by quantMSImageR", "concept": [ "visualisation" ], "topics": [ "quant_palettes" ] }, { "page": "quantile_hm", "title": "Quantile heatmap of MSI features across samples", "concept": [ "visualisation" ], "topics": [ "quantile_hm" ] }, { "page": "quantMSImageR-accessors", "title": "Accessors for calibration and tissue metadata", "concept": [ "accessors" ], "topics": [ "calibrationData", "calibrationData,quant_MSImagingExperiment-method", "calibrationData<-", "calibrationData<-,quant_MSImagingExperiment-method", "calibrationDiagnostics", "calibrationDiagnostics,quant_MSImagingExperiment-method", "calibrationLevels", "calibrationLevels,quant_MSImagingExperiment-method", "calibrationMetadata", "calibrationMetadata,quant_MSImagingExperiment-method", "calibrationModels", "calibrationModels,quant_MSImagingExperiment-method", "calibrationModels<-", "calibrationModels<-,quant_MSImagingExperiment-method", "calibrationR2", "calibrationR2,quant_MSImagingExperiment-method", "quantMSImageR-accessors", "tissueData", "tissueData,quant_MSImagingExperiment-method", "tissueMatrix", "tissueMatrix,quant_MSImagingExperiment-method" ] }, { "page": "read_mrm", "title": "Read a Waters DESI-MRM acquisition into an MSImagingExperiment", "concept": [ "acquisition" ], "topics": [ "read_mrm" ] }, { "page": "remove_blank_mzs-quant_MSImagingExperiment-method", "title": "Remove features without observed signal", "concept": [ "acquisition" ], "topics": [ "remove_blank_mzs", "remove_blank_mzs,quant_MSImagingExperiment-method" ] }, { "page": "run_example", "title": "Run the quantMSImageR example study", "concept": [ "workflow" ], "topics": [ "run_example" ] }, { "page": "run_study", "title": "Run a full DESI-MRM study from a YAML configuration", "concept": [ "workflow" ], "topics": [ "run_study" ] }, { "page": "select_tissue_pixels", "title": "Interactively select tissue pixels for an acquisition", "concept": [ "acquisition" ], "topics": [ "select_tissue_pixels" ] }, { "page": "summarise_cal_levels-quant_MSImagingExperiment-method", "title": "Summarise the response at each calibration level", "concept": [ "calibration" ], "topics": [ "summarise_cal_levels", "summarise_cal_levels,quant_MSImagingExperiment-method" ] }, { "page": "tissueInfo-class", "title": "Tissue-level summaries for an imaging experiment", "topics": [ "tissueInfo", "tissueInfo-class" ] }, { "page": "trim_MSI", "title": "Remove pure-background border rows and columns from an MSI object", "concept": [ "acquisition" ], "topics": [ "trim_MSI" ] }, { "page": "validate_config", "title": "Validate a study YAML configuration", "concept": [ "workflow" ], "topics": [ "validate_config" ] }, { "page": "zero2na-quant_MSImagingExperiment-method", "title": "Replace zero intensities with NA", "concept": [ "filtering" ], "topics": [ "zero2na", "zero2na,quant_MSImagingExperiment-method" ] } ], "_pkglogo": "https://github.com/BiocStaging/quantMSImageR/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/BiocStaging/quantMSImageR/raw/HEAD/README.md", "_rundeps": [ "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "bslib", "cachem", "Cardinal", "CardinalIO", "chemCal", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "digest", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GetoptLong", "ggplot2", "GlobalOptions", "glue", "gridExtra", "gtable", "highr", "htmltools", "IRanges", "irlba", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "matter", "memoise", "mime", "nlme", "ontologyIndex", "patchwork", "pillar", "pkgconfig", "png", "pracma", "ProtGenerics", "purrr", "R6", "rappdirs", "RColorBrewer", "rjson", "rlang", "rmarkdown", "S4Vectors", "S7", "sass", "scales", "shape", "snow", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "quantMSImageR.Rmd", "filename": "quantMSImageR.html", "title": "Introduction to quantMSImageR", "author": "Matthew J. Smith", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "What this package does", "Scope", "The workflow", "Installation", "Quick start", "The data model", "Reading your own data", "Loading the acquisitions", "Selecting tissue pixels", "Ion images", "Colour-scale treatment", "Quantile heatmaps across samples", "Signal-to-noise filtering", "Running a full study from a YAML config", "The configuration as a record of the analysis", "References", "Session information" ], "created": "2026-07-20 14:02:25", "modified": "2026-07-23 16:39:29", "commits": 17 }, { "source": "quantification.Rmd", "filename": "quantification.html", "title": "Quantification with calibration standards", "author": "Matthew J. Smith", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "On-slide versus on-tissue calibration", "Scope and assumptions", "Installation", "Calibration workflow overview", "The bundled calibration dataset", "Fitting and diagnosing calibration models", "R² is not enough", "Applying the models to a study section", "Checking calibration coverage", "Handling out-of-range pixels", "Driving calibration from a study YAML", "Interpretation and limitations", "References", "Session information" ], "created": "2026-07-20 16:40:26", "modified": "2026-07-23 16:39:29", "commits": 10 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "quantmsimager", "_universes": [ "biocstaging", "mjs-708" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-07-23T18:59:44.000Z", "distro": "resolute", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/70bcca48f09920da6236401ea2bedaee54e6c73a174e9fb248c6ee40f2103e34", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.6.1", "os": "linux", "version": "0.99.0", "date": "2026-07-23T18:59:38.000Z", "distro": "resolute", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/9e78fc870254cb6e9fd3110f7b7fa3b6c8b6ed14273d5ced961178acbb8592e8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-07-23T18:58:12.000Z", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/0e26af387f3de66f4199eba2b0e8a2862aa804f4b728d190829f375d5b8a1178", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.6.1", "os": "mac", "version": "0.99.0", "date": "2026-07-23T18:58:33.000Z", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/eb71207d1a4c4611dfb70efe60742aae11804757deaac8ba5bba368317ae0ec6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-07-23T18:59:50.000Z", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/5f2ac49c887d3e694154de17555e7853ca5dc5bc748a252374303fe9eaafa7d2", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-07-23T18:58:21.000Z", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/f282287db1ce66a7e6ef7b1d1604627c4fef9f3ee8a2901ffaaf86315eb071f9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-07-23T18:58:32.000Z", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/2d2d0a6f802b93ae172973c19eed40bc841f0a90848f1171c50a3809cb6d077d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" }, { "r": "4.6.1", "os": "win", "version": "0.99.0", "date": "2026-07-23T18:58:33.000Z", "commit": "8be881d9e298069154b9d4bf39caf59e68d27c08", "fileid": "https://r2.ropensci.org/123fd428bf1db63c64224ba30723cc34271dd3cdce8e28e0e070b73ccd32ea30", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30035512066" } ] }