{ "_id": "6a103044acfb0bcc41c955a3", "Package": "Chromatograms", "Title": "Infrastructure for Chromatographic Mass Spectrometry Data", "Version": "1.3.0", "Description": "The Chromatograms packages defines an efficient\ninfrastructure for storing and handling of chromatographic mass\nspectrometry data. It provides different implementations of\n*backends* to store and represent the data. Such backends can\nbe optimized for small memory footprint or fast data\naccess/processing. A lazy evaluation queue and chunk-wise\nprocessing capabilities ensure efficient analysis of also very\nlarge data sets.", "Authors@R": "c(person(given = \"Johannes\", family = \"Rainer\",\nemail = \"Johannes.Rainer@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Laurent\", family = \"Gatto\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nemail = \"laurent.gatto@uclouvain.be\",\nrole = c(\"aut\")),\nperson(given = \"Philippine\", family = \"Louail\",\nemail = \"philippine.louail@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0007-5429-6846\",\nfnd = \"European Union HORIZON-MSCA-2021 project\nGrant No. 101073062: HUMAN – Harmonising and Unifying Blood\nMetabolic Analysis Networks\")))", "License": "Artistic-2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "BugReports": "https://github.com/RforMassSpectrometry/Chromatograms/issues", "URL": "https://github.com/RforMassSpectrometry/Chromatograms", "biocViews": "Infrastructure, Metabolomics, MassSpectrometry, Proteomics", "Roxygen": "list(markdown=TRUE)", "RoxygenNote": "7.3.3", "Collate": "'AllGenerics.R' 'ChromBackend-functions.R' 'ChromBackend.R'\n'hidden_aliases.R' 'helpers.R' 'ChromBackendMemory.R'\n'ChromBackendMzR.R' 'ChromBackendSpectra.R' 'Chromatograms.R'\n'Chromatograms-chromData.R' 'Chromatograms-peaksData.R'\n'Chromatograms-plot.R' 'Chromatograms-processingQueue.R'", "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:23 UTC", "RemoteUrl": "https://github.com/bioc/Chromatograms", "RemoteRef": "HEAD", "RemoteSha": "31a1ba2730854e735522936c7c345eeea5ff9189", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 09:37:40 UTC", "User": "root" }, "Author": "Johannes Rainer [aut] (ORCID: ),\nLaurent Gatto [aut] (ORCID: ),\nPhilippine Louail [aut, cre] (ORCID:\n, fnd: European Union\nHORIZON-MSCA-2021 project Grant No. 101073062: HUMAN – Harmonising\nand Unifying Blood Metabolic Analysis Networks)", "Maintainer": "Philippine Louail ", "MD5sum": "316a7956ca8ad80a9c4946b2cad49561", "_user": "bioc", "_type": "src", "_file": "Chromatograms_1.3.0.tar.gz", "_fileid": "2273e2da82e1e933cec1c93e0404aeabee584616f96083b5edbae4cdc8ba2e54", "_filesize": 700584, "_sha256": "2273e2da82e1e933cec1c93e0404aeabee584616f96083b5edbae4cdc8ba2e54", "_created": "2026-05-12T09:37:40.000Z", "_published": "2026-05-22T10:30:28.084Z", "_jobs": [ { "job": 77361954448, "time": 211, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "6940754085" }, { "job": 77361954950, "time": 309, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6940788019" }, { "job": 77361954628, "time": 283, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6940781515" }, { "job": 77361954847, "time": 211, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6940836829" }, { "job": 77361954913, "time": 239, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6940846168" }, { "job": 77361954105, "time": 261, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6940676035" }, { "job": 77361954063, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158379548" }, { "job": 77361954390, "time": 307, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6940787583" }, { "job": 77361954863, "time": 301, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6940785409" }, { "job": 77361954675, "time": 309, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6940787922" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Chromatograms", "_commit": { "id": "31a1ba2730854e735522936c7c345eeea5ff9189", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381523 }, "_maintainer": { "name": "Philippine Louail", "email": "philippine.louail@outlook.com", "login": "philouail", "uuid": 127301965 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "BiocParallel", "role": "Depends" }, { "package": "ProtGenerics", "version": ">= 1.39.2", "role": "Depends" }, { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "MsCoreUtils", "version": ">= 1.7.5", "role": "Imports" }, { "package": "Spectra", "role": "Imports" }, { "package": "msdata", "version": ">= 0.19.3", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "BiocStyle", "version": ">= 2.5.19", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.1.0", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "mzR", "version": ">= 2.41.4", "role": "Suggests" }, { "package": "MsBackendMetaboLights", "version": ">= 1.3.1", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-22", "n": 1 }, { "week": "2025-29", "n": 2 }, { "week": "2025-38", "n": 1 }, { "week": "2025-39", "n": 1 }, { "week": "2025-40", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2026-04", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-10", "n": 1 }, { "week": "2026-11", "n": 1 }, { "week": "2026-12", "n": 1 }, { "week": "2026-14", "n": 2 }, { "week": "2026-16", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "metabolomics", "massspectrometry", "proteomics" ], "_stars": 2, "_contributors": [ { "user": "philouail", "count": 121, "uuid": 127301965 }, { "user": "jorainer", "count": 58, "uuid": 5506112 }, { "user": "lgatto", "count": 15, "uuid": 384198 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 197, "source": "https://www.bioconductor.org/packages/stats/bioc/Chromatograms" }, "_devurl": "https://github.com/rformassspectrometry/chromatograms", "_searchresults": 26, "_rbuild": "4.6.0", "_assets": [ "extra/Chromatograms.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rformassspectrometry/chromatograms", "_realowner": "bioc", "_cranurl": false, "_exports": [ "applyProcessing", "backendBpparam", "backendInitialize", "backendMerge", "backendParallelFactor", "Chromatograms", "ChromBackendMemory", "ChromBackendMzR", "ChromBackendSpectra", "chromData", "chromData<-", "chromExtract", "chromIndex", "chromIndex<-", "chromSpectraIndex", "chromVariables", "collisionEnergy", "collisionEnergy<-", "compareChromatograms", "concatenateChromatograms", "coreChromVariables", "corePeaksVariables", "dataOrigin", "dataOrigin<-", "extractByIndex", "factorize", "fillCoreChromVariables", "filterChromData", "filterEmptyChromatograms", "filterPeaksData", "imputePeaksData", "intensity", "intensity<-", "isEmpty", "isReadOnly", "matchRtime", "msLevel", "msLevel<-", "mz", "mz<-", "mzMax", "mzMax<-", "mzMin", "mzMin<-", "peakBoundary", "peaksData", "peaksData<-", "plotChromatograms", "plotChromatogramsOverlay", "precursorMz", "precursorMz<-", "precursorMzMax", "precursorMzMax<-", "precursorMzMin", "precursorMzMin<-", "processingChunkFactor", "processingChunkSize", "processingChunkSize<-", "productMz", "productMz<-", "productMzMax", "productMzMax<-", "productMzMin", "productMzMin<-", "reset", "rtime", "rtime<-", "setBackend", "show", "split", "supportsSetBackend", "validChromData", "validPeaksData" ], "_help": [ { "page": "Chromatograms", "title": "The Chromatograms class to manage and access chromatographic data", "topics": [ "$,Chromatograms-method", "$<-,Chromatograms-method", "Chromatograms", "Chromatograms,ChromBackendOrMissing-method", "Chromatograms,Spectra-method", "Chromatograms-class", "chromExtract", "chromExtract,Chromatograms-method", "factorize,Chromatograms-method", "filterEmptyChromatograms", "filterEmptyChromatograms,Chromatograms-method", "setBackend,Chromatograms,ChromBackend-method", "[,Chromatograms-method", "[<-,Chromatograms-method", "[[,Chromatograms-method", "[[<-,Chromatograms-method" ] }, { "page": "ChromBackendMemory", "title": "Improved in-memory Chromatographic data backend", "topics": [ "backendInitialize,ChromBackendMemory-method", "ChromBackendMemory" ] }, { "page": "ChromBackendMzR", "title": "Chromatographic Data Backend for Reading mzML Files", "topics": [ "backendInitialize,ChromBackendMzR-method", "ChromBackendMzR" ] }, { "page": "ChromBackendSpectra", "title": "Chromatographic Data Backend for Spectra Objects", "topics": [ "backendInitialize,ChromBackendSpectra-method", "ChromBackendSpectra", "chromSpectraIndex" ] }, { "page": "chromData", "title": "Chromatographic Peaks Metadata.", "topics": [ "chromData", "chromData,Chromatograms-method", "chromData<-", "chromData<-,Chromatograms-method", "chromIndex", "chromIndex,Chromatograms-method", "chromIndex<-", "chromIndex<-,Chromatograms-method", "chromVariables", "chromVariables,Chromatograms-method", "chromVariables<-", "collisionEnergy", "collisionEnergy,Chromatograms-method", "collisionEnergy<-", "collisionEnergy<-,Chromatograms-method", "dataOrigin", "dataOrigin,Chromatograms-method", "dataOrigin<-", "dataOrigin<-,Chromatograms-method", "filterChromData", "filterChromData,Chromatograms-method", "length,Chromatograms-method", "msLevel", "msLevel,Chromatograms-method", "msLevel<-", "msLevel<-,Chromatograms-method", "mz", "mz,Chromatograms-method", "mz<-", "mz<-,Chromatograms-method", "mzMax", "mzMax,Chromatograms-method", "mzMax<-", "mzMax<-,Chromatograms-method", "mzMin", "mzMin,Chromatograms-method", "mzMin<-", "mzMin<-,Chromatograms-method", "precursorMz", "precursorMz,Chromatograms-method", "precursorMz<-", "precursorMz<-,Chromatograms-method", "precursorMzMax", "precursorMzMax,Chromatograms-method", "precursorMzMax<-", "precursorMzMax<-,Chromatograms-method", "precursorMzMin", "precursorMzMin,Chromatograms-method", "precursorMzMin<-", "precursorMzMin<-,Chromatograms-method", "productMz", "productMz,Chromatograms-method", "productMz<-", "productMz<-,Chromatograms-method", "productMzMax", "productMzMax,Chromatograms-method", "productMzMax<-", "productMzMax<-,Chromatograms-method", "productMzMin", "productMzMin,Chromatograms-method", "productMzMin<-", "productMzMin<-,Chromatograms-method" ] }, { "page": "concatenateChromatograms", "title": "Merging, combining and splitting Chromatograms", "topics": [ "c,Chromatograms-method", "concatenateChromatograms", "split,Chromatograms,ANY-method" ] }, { "page": "ChromBackend", "title": "Chromatographic MS Data Backends", "topics": [ "$,ChromBackend-method", "$<-,ChromBackend-method", "backendBpparam,ChromBackend-method", "backendInitialize,ChromBackend-method", "backendMerge,ChromBackend-method", "backendMerge,list-method", "backendParallelFactor,ChromBackend-method", "ChromBackend", "ChromBackend-class", "ChromBackendMemory-class", "ChromBackendMzR-class", "ChromBackendSpectra-class", "chromData,ChromBackend-method", "chromData<-,ChromBackend-method", "chromExtract,ChromBackend-method", "chromIndex,ChromBackend-method", "chromIndex<-,ChromBackend-method", "chromVariables,ChromBackend-method", "collisionEnergy,ChromBackend-method", "collisionEnergy<-,ChromBackend-method", "coreChromVariables", "corePeaksVariables", "dataOrigin,ChromBackend-method", "dataOrigin<-,ChromBackend-method", "extractByIndex", "extractByIndex,ChromBackend,ANY-method", "extractByIndex,ChromBackend,missing-method", "factorize", "factorize,ChromBackend-method", "filterChromData,ChromBackend-method", "filterEmptyChromatograms,ChromBackend-method", "filterPeaksData,ChromBackend-method", "imputePeaksData,ChromBackend-method", "intensity,ChromBackend-method", "intensity<-,ChromBackend-method", "isEmpty,ChromBackend-method", "isReadOnly,ChromBackend-method", "length,ChromBackend-method", "lengths,ChromBackend-method", "msLevel,ChromBackend-method", "msLevel<-,ChromBackend-method", "mz,ChromBackend-method", "mz<-,ChromBackend-method", "mzMax,ChromBackend-method", "mzMax<-,ChromBackend-method", "mzMin,ChromBackend-method", "mzMin<-,ChromBackend-method", "peaksData,ChromBackend-method", "peaksData<-,ChromBackend-method", "peaksVariables,ChromBackend-method", "precursorMz,ChromBackend-method", "precursorMz<-,ChromBackend-method", "precursorMzMax,ChromBackend-method", "precursorMzMax<-,ChromBackend-method", "precursorMzMin,ChromBackend-method", "precursorMzMin<-,ChromBackend-method", "productMz,ChromBackend-method", "productMz<-,ChromBackend-method", "productMzMax,ChromBackend-method", "productMzMax<-,ChromBackend-method", "productMzMin,ChromBackend-method", "productMzMin<-,ChromBackend-method", "reset,ChromBackend-method", "rtime,ChromBackend-method", "rtime<-,ChromBackend-method", "split,ChromBackend,ANY-method", "supportsSetBackend,ChromBackend-method", "[,ChromBackend-method", "[[,ChromBackend-method", "[[<-,ChromBackend-method" ] }, { "page": "peaksData", "title": "Chromatographic peaks data", "topics": [ "compareChromatograms", "compareChromatograms,Chromatograms,Chromatograms-method", "compareChromatograms,Chromatograms,missing-method", "filterPeaksData", "filterPeaksData,Chromatograms-method", "imputePeaksData", "imputePeaksData,Chromatograms-method", "intensity,Chromatograms-method", "intensity<-,Chromatograms-method", "lengths,Chromatograms-method", "matchRtime", "peakBoundary", "peakBoundary,Chromatograms-method", "peaksData", "peaksData,Chromatograms-method", "peaksData<-,Chromatograms-method", "peaksVariables", "peaksVariables,Chromatograms-method", "rtime,Chromatograms-method", "rtime<-,Chromatograms-method" ] }, { "page": "plotChromatograms", "title": "Plot chromatograms", "topics": [ "plotChromatograms", "plotChromatogramsOverlay" ] }, { "page": "processingQueue", "title": "Efficiently processing 'Chromatograms' objects.", "topics": [ "addProcessing,Chromatograms-method", "applyProcessing,Chromatograms-method", "processingChunkFactor,Chromatograms-method", "processingChunkSize,Chromatograms-method", "processingChunkSize<-,Chromatograms-method", "processingQueue" ] } ], "_readme": "https://github.com/bioc/Chromatograms/raw/HEAD/README.md", "_rundeps": [ "BH", "BiocGenerics", "BiocParallel", "clue", "cluster", "codetools", "cpp11", "data.table", "formatR", "fs", "futile.logger", "futile.options", "generics", "IRanges", "lambda.r", "MASS", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "Rcpp", "S4Vectors", "snow", "Spectra" ], "_vignettes": [ { "source": "creating-backend-classes.Rmd", "filename": "creating-backend-classes.html", "title": "Creating new ChromBackend classes for Chromatograms", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "What is a ChromBackend?", "Conventions and definitions", "Notes on parallel and chunk-wise processing", "API", "Required methods", "dataStorage()", "length()", "backendInitialize()", "chromVariables()", "chromData()", "peaksVariables()", "peaksData()", "[", "$", "backendMerge()", "Data replacement methods", "chromData<-", "$<-", "peaksData<-", "Methods with available default implementations", "backendParallelFactor()", "chromIndex()", "collisionEnergy()", "dataOrigin(), dataOrigin<-", "intensity(), intensity<-", "isEmpty()", "isReadOnly()", "lengths()", "msLevel(), msLevel<-", "mz(), mz<-", "mzMax(), mzMax<-", "mzMin(), mzMin<-`", "precursorMz(), precursorMz<-", "precursorMzMax(), precursorMzMax<-", "precursorMzMin(), precursorMzMin<-", "productMz(), productMz<-", "productMzMax(), productMzMax<-", "productMzMin(), productMzMin<-", "rtime(), rtime<-", "split()", "Session information" ], "created": "2024-03-27 07:29:10", "modified": "2025-07-14 12:10:13", "commits": 6 }, { "source": "using-a-chromatograms-object.Rmd", "filename": "using-a-chromatograms-object.html", "title": "Using and understanding a Chromatograms object", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "The Chromatograms object", "Available backends", "Chromatographic peaks data", "Chromatograms metadata", "Creating Chromatograms objects", "Access data from a Chromatograms object", "peaksData", "chromData", "Lazy Processing and Parallelization", "Processing queue", "Parallelization", "Changing backend type", "Choosing the right backend", "Plotting chromatograms from a Spectra object", "Understanding Factorization", "Re-factorizing after metadata changes", "Extracting chromatographic regions of interest", "Basic extraction by retention time", "Extraction with m/z filtering (ChromBackendSpectra only)", "Imputing missing values in chromatograms", "Available imputation methods", "Extrapolation vs. Interpolation", "Example: Imputing an extracted ion chromatogram (EIC)", "Selecting the right imputation method", "Imputation in lazy evaluation pipelines", "Comparing chromatograms", "Comparing chromatograms within a single object", "Comparing two Chromatograms objects", "Comparing groups of chromatograms", "Session information" ], "created": "2025-02-18 08:10:12", "modified": "2026-04-02 11:04:41", "commits": 10 } ], "_score": 6.816373888752362, "_indexed": true, "_nocasepkg": "chromatograms", "_universes": [ "bioc", "philouail", "rformassspectrometry" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-12T09:41:26.000Z", "distro": "noble", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "900d7cffe4dd2b22f5c562c90a40d20ae88e7e9ef82134b0a382dd7b03ae9a54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-12T09:41:09.000Z", "distro": "noble", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "144dcb80c56bf0f71fe076da0cd25f1ab92b4c45fbec7882eeeec15498ffc5b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-12T09:44:05.000Z", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "0e05d88dd1fece3aeb270671e2d3ca5923b3e2cd4dc01ced1cfd756c5736dcd7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-12T09:43:55.000Z", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "e8b17f4073b07883824bd5aa735dcf0c0c6e02def93be6a066786eaaadb87908", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-12T09:39:47.000Z", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "a730d97eda51a8ab192a3827c42369c0d76c8a56461a35c07060ed6a26518f2d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-12T09:39:46.000Z", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "247adf5cc55376bdfeb64ea345907db1bc1bb1cf5ef2c845f1e17caa35b141b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-12T09:39:39.000Z", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "b11628746b6455f2b234d75f479235e8b34cd00bfdfe4598c5d1eababb212d77", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-22T10:30:06.000Z", "commit": "31a1ba2730854e735522936c7c345eeea5ff9189", "fileid": "c27c3511ac8f50cd2b9702df7393ec9887a2daf8712361b919bbca9a60f7d1ab", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726019393" } ] }