{ "_id": "6a0f732aacfb0bcc41c603a6", "Package": "PepMapViz", "Title": "A Versatile Toolkit for Peptide Mapping, Visualization, and\nComparative Exploration", "Version": "1.1.0", "Authors@R": "c(\nperson(given = \"Zhenru\", family = \"Zhou\", email = \"zhou.zhenru@gene.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Qui\", family = \"Phung\", email = \"phung.qui@gene.com\", role = c(\"aut\")),\nperson(given = \"Corey\", family = \"Bakalarski\", email = \"bakalarski.corey@gene.com\", role = c(\"aut\")))", "Description": "A versatile R visualization package that empowers\nresearchers with comprehensive visualization tools for\nseamlessly mapping peptides to protein sequences, identifying\ndistinct domains and regions of interest, accentuating\nmutations, and highlighting post-translational modifications,\nall while enabling comparisons across diverse experimental\nconditions. Potential applications of 'PepMapViz' include the\nvisualization of cross-software mass spectrometry results at\nthe peptide level for specific protein and domain details in a\nlinearized format and post-translational modification coverage\nacross different experimental conditions; unraveling insights\ninto disease mechanisms. It also enables visualization of Major\nhistocompatibility complex-presented peptide clusters in\ndifferent antibody regions predicting immunogenicity in\nantibody drug development.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Note": "The package 'MSnbase' is used for parsing and processing mzTab\nfiles. While its non-portability limits usage on some\nplatforms, it is essential for enabling analysis and\nintegration of mzTab data in 'PepMapViz'. However, if the input\nfile is not in mzTab format, 'MSnbase' is not required, and the\npackage can function without it.", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "biocViews": "Immunogenicity, MassSpectrometry, Proteomics, Peptidomics,\nSoftware, Visualization", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 06:41:39 UTC", "User": "root" }, "Author": "Zhenru Zhou [aut, cre], Qui Phung [aut], Corey Bakalarski [aut]", "Maintainer": "Zhenru Zhou ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-06-25 17:10:06 UTC", "RemoteUrl": "https://github.com/cran/PepMapViz", "RemoteRef": "HEAD", "RemoteSha": "f357c66dca8a14b981fb8164428988690e6aef97", "MD5sum": "d0016355a432626d48f1a9f6c16b9aa4", "_user": "cran", "_type": "src", "_file": "PepMapViz_1.1.0.tar.gz", "_fileid": "44d6b0bbef0872fcafa853820819da98ca25f1e1203b49b50a051ceb2dfd4133", "_filesize": 647972, "_sha256": "44d6b0bbef0872fcafa853820819da98ca25f1e1203b49b50a051ceb2dfd4133", 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"zhou.zhenru@gene.com" }, "_registered": true, "_dependencies": [ { "package": "shiny", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "ggforce", "role": "Imports" }, { "package": "ggh4x", "role": "Imports" }, { "package": "ggnewscale", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "mzID", "role": "Suggests" }, { "package": "MSnbase", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 1 } ], "_tags": [ { "name": "1.1.0", "date": "2025-06-25" } ], "_topics": [ "immunogenicity", "massspectrometry", "proteomics", "peptidomics", "software", "visualization" ], "_stars": 1, 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"obtain_mod_Spectronaut" ] }, { "page": "peptide_quantification", "title": "Peptide Quantification", "topics": [ "peptide_quantification" ] }, { "page": "run_pepmap_app", "title": "Launch PepMapViz Shiny Application", "topics": [ "run_pepmap_app" ] }, { "page": "strip_sequence", "title": "Strip peptide sequences based on the specified data type", "topics": [ "strip_sequence" ] }, { "page": "strip_sequence_Comet", "title": "Strip sequence from Comet outputs", "topics": [ "strip_sequence_Comet" ] }, { "page": "strip_sequence_DIANN", "title": "Strip sequence from DIANN outputs", "topics": [ "strip_sequence_DIANN" ] }, { "page": "strip_sequence_Maxquant", "title": "Strip sequence from Maxquant outputs", "topics": [ "strip_sequence_Maxquant" ] }, { "page": "strip_sequence_MSFragger", "title": "Strip sequence from MSFragger outputs", "topics": [ "strip_sequence_MSFragger" ] }, { "page": "strip_sequence_PEAKS", "title": "Strip sequence from PEAKS outputs", "topics": [ "strip_sequence_PEAKS" ] 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