{ "_id": "6acb6c4cfe5cc25786e8fd2f", "Package": "ProteinBatcher", "Title": "An end-to-end proteomics workflow with condition-aware\nimputation, flexible statistical modelling and interactive\nvisualization", "Version": "0.99.7", "Authors@R": "c(person(given = \"Aitor\", family =\"Moruno-Cuenca\", email = \"morunoaitor@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0009-8133-2552\")),\nperson(given = \"Dr. Sergi\", family = \"Sayols-Puig\", email = \"sergi.sayolspuig@almirall.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-3877-4170\")),\nperson(given = \"Dr. Bruna\", family = \"Oriol-Tordera\", email = \"bruna.orioltordera@almirall.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-2714-9097\")),\nperson(given = \"Dr. Hiba\", family = \"Salim\", email = \"hiba.salim@crg.eu\", role = c(\"dtc\"), comment = c(ORCID = \"0000-0002-2168-0258\")),\nperson(given = \"Dr. Francesc\", family = \"Fernández-Albert\", email = \"francesc.fernandez@almirall.com\", role = c(\"ths\"), comment = c(ORCID = \"0000-0001-5561-0701\")),\nperson(given = \"Prof. Dr. Alexandre\", family = \"Perera-Lluna\", email = \"alexandre.perera@upc.edu\", role = c(\"ths\"), comment = c(ORCID = \"0000-0001-6427-851X\")),\nperson(given = \"Dr. Guadalupe\", family = \"Espadas-García\", email = \"guadalupe.espadas@crg.eu\", role = c(\"ctb\", \"dtc\"), comment = c(ORCID = \"0000-0002-6415-8013\")),\nperson(given = \"Dr. Elisa\", family = \"Monzón-Casanova\", email = \"elisa.monzoncasanova@almirall.com\", role = c(\"ctb\", \"fnd\"), comment = c(ORCID = \"0000-0001-6617-6138\")),\nperson(given = \"Prof. Dr. Eduard\", family = \"Sabidó-Aguade\", email = \"eduard.sabido@upf.edu\", role = c(\"res\", \"ctb\", \"dtc\", \"fnd\"), comment = c(ORCID = \"0000-0001-6506-7714\")))", "Description": "ProteinBatcher provides utilities to read, validate, and\nharmonize quantitative proteomics result tables generated by\nDIA-NN from data-independent acquisition mass spectrometry\nexperiments. The package enables batch processing of multiple\nDIA-NN output files, consistent handling of protein identifiers\nand associated metadata, and transformation of tabular data\ninto analysis-ready formats. It facilitates downstream\ndifferential abundance analysis using linear modeling\nframeworks based on limma, with explicit support for\nmultivariable experimental designs including batch effects and\nother confounding covariates, as well as correlation-aware\ndesigns via duplicateCorrelation.", "License": "MIT + file LICENSE", "URL": "https://github.com/DataScienceRD-Almirall/ProteinBatcher", "BugReports": "https://github.com/DataScienceRD-Almirall/ProteinBatcher/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "biocViews": "Proteomics, MassSpectrometry, DataImport,\nDataRepresentation, Software, BatchEffect", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-21 16:59:35 UTC", "RemoteUrl": "https://github.com/bioc/ProteinBatcher", "RemoteRef": "HEAD", "RemoteSha": "1c6df35e6b9a0f0f333f23521ff00b7bd5ff508f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-11 10:32:28 UTC", "User": "root" }, "Author": "Aitor Moruno-Cuenca [aut, cre] (ORCID:\n),\nDr. Sergi Sayols-Puig [ctb] (ORCID:\n),\nDr. Bruna Oriol-Tordera [ctb] (ORCID:\n),\nDr. Hiba Salim [dtc] (ORCID: ),\nDr. Francesc Fernández-Albert [ths] (ORCID:\n),\nProf. Dr. Alexandre Perera-Lluna [ths] (ORCID:\n),\nDr. Guadalupe Espadas-García [ctb, dtc] (ORCID:\n),\nDr. Elisa Monzón-Casanova [ctb, fnd] (ORCID:\n),\nProf. Dr. Eduard Sabidó-Aguade [res, ctb, dtc, fnd] (ORCID:\n)", "Maintainer": "Aitor Moruno-Cuenca ", "_user": "bioc", "_type": "src", "_file": "ProteinBatcher_0.99.7.tar.gz", "_fileid": "https://r2.ropensci.org/da787b6f07d7508820ab4c8dc9fda94fd74dc33162210dfb5215eb4a33eca636", "_filesize": 6797706, "_sha256": "da787b6f07d7508820ab4c8dc9fda94fd74dc33162210dfb5215eb4a33eca636", "_expires": "2027-01-19T11:00:26.000Z", "_created": "2026-10-11T10:32:28.000Z", "_published": "2026-10-11T11:00:28.263Z", "_buildurl": 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