{ "_id": "6ad13ddf0edca5be25021afd", "Package": "quantMSImageR", "Title": "Processing and Quantification of Targeted Mass Spectrometry\nImaging Data", "Version": "0.99.10", "Authors@R": "person(c(\"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' 'alignFeatures.R' 'applySNR.R'\n'back2NA.R' 'bindPanels.R' 'blockCentre.R' 'buildFeatureMeta.R'\n'combineMSIs.R' 'contributionHm.R' 'createCalCurve.R'\n'createMSIDataMatrix.R' 'generateTxtImages.R' 'imageR.R'\n'int2SNR.R' 'int2conc.R' 'int2response.R' 'join_ion_library.R'\n'labelROIs.R' 'palettes.R' 'plotCalCoverage.R'\n'quantMSImageR-package.R' 'quantileHm.R' 'readMRM.R'\n'removeBlankMzs.R' 'runExample.R' 'runStudy.R'\n'selectTissuePixels.R' 'stitchAcquisitions.R'\n'summariseCalLevels.R' 'trimMSI.R' 'validate.R' 'zero2NA.R'", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev perl", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-15 17:12:57 UTC", "RemoteUrl": "https://github.com/bioc/quantMSImageR", "RemoteRef": "HEAD", "RemoteSha": "d1987f264383c7995d80b8a3679670ddb1d9e366", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 20:39:23 UTC", "User": "root" }, "Author": "Matthew J. Smith [aut, cre] (ORCID:\n)", "Maintainer": "Matthew J. Smith ", "_user": "bioc", "_type": "src", "_file": "quantMSImageR_0.99.10.tar.gz", "_fileid": "https://r2.ropensci.org/49ea743728da3dd3e2c7c381821deefa09284d89b4f86fa1f053e092059a95b2", "_filesize": 1991907, "_sha256": "49ea743728da3dd3e2c7c381821deefa09284d89b4f86fa1f053e092059a95b2", "_expires": "2027-01-23T20:55:56.000Z", "_created": "2026-10-15T20:39:23.000Z", "_published": "2026-10-15T20:55:59.750Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38802985245", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 13 }, "_upstream": "https://github.com/bioc/quantMSImageR", "_commit": { "id": "d1987f264383c7995d80b8a3679670ddb1d9e366", "author": "Matthew Smith ", "committer": "Matthew Smith ", "message": "Version 0.99.10: blocking, per-block ion images, stitch overlap\n\nCorrect a study for a factor that is not the comparison -- the patient a\npaired set of treatments came from, the sex of an animal, the slide an\nacquisition sat on.\n\n* `block:` names that factor per sample, beside the `group:` being compared.\n `parameters: block_centre:` decides what to do about it: `center` divides\n each feature by the block's own geometric mean, `baseline` by its\n `baseline_group` arm so a value reads as a fold change against its own\n control. `off` is the default, so declaring a block changes no number on\n its own. The correction is multiplicative, so a block's gain goes and the\n size of its response stays. It reaches the heatmaps and the comparison\n plots; the ion images stay uncorrected, because an image should show the\n intensity that was measured. A corrected report says so and gains\n `blocked` in its filename. `blockCentre()` is exported.\n\n* `output: ion_images:` collects the display settings every image in the\n report shares. `percentile:` is the cap -- previously the animation was\n fixed at 95, the dropdown computed its own, and the concentration images\n silently took 99. `scale_within:` gives each block its own colour scale,\n drawn as one column per block with its groups as rows and replicates\n across, each column stating the value it is capped at.\n\n* `stitchAcquisitions(overlap = )` and `parameters: stitch_overlap:` for\n pieces of one tissue that share a strip. `error` stays the default.\n\n* `fData()` carries `collision_eV` and `cone_V`, so the feature table tells\n two transitions apart without a trip to the raw data.\n\n* A sample's group is given by `group:` rather than `label:`, and\n `baseline_label:` by `baseline_group:`. Both old names keep working and\n `validateConfig()` says how many samples still use them.\n\n* `heatmap_style: auto` no longer picks the contribution heatmap when the\n z-score behind it cannot resolve anything: that score is taken within a", "time": 1792084377 }, "_maintainer": { "name": "Matthew J. 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"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": "labelROIs", "title": "Label regions of interest within the tissue of an acquisition", "concept": [ "acquisition" ], 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