{ "_id": "6aca7a86fe5cc25786e89e6e", "Package": "pepVet", "Type": "Package", "Title": "Evaluate Proteolytic Digests for Proteomics Workflows", "Version": "0.99.1", "Authors@R": "person(\"Enes K. Ergin\", email = \"eneskemalergin@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9810-7399\"))", "Description": "Simulates proteolytic digestion, scores the resulting\npeptides for LC-MS/MS suitability, compares candidate enzymes,\nand reports digest quality at the protein level. Supports 40\ncleaver-compatible enzyme rules, workflow presets, peptide mass\nand pI calculations, sequence-local cleavage-efficiency\nannotations, and proteome-aware uniqueness scoring. Evaluates\nmulti-FASTA files in batches with per-protein triage and\nproteome-level summaries. Exports peptide lists for Skyline and\ngeneric downstream tools and prints styled console reports.", "License": "MIT + file LICENSE", "URL": "https://github.com/LangeLab/pepVet,\nhttps://langelab.github.io/pepVet/", "BugReports": "https://github.com/LangeLab/pepVet/issues", "VignetteBuilder": "knitr", "biocViews": "Proteomics, MassSpectrometry, QualityControl", "Encoding": "UTF-8", "Config/Needs/build": "BiocStyle, ggplot2, knitr, patchwork, rmarkdown", "Config/Needs/check": "rcmdcheck", "Config/Needs/coverage": "covr, ggplot2, patchwork, ragg, testthat (>=\n3.0.0), withr, xml2", "Config/Needs/lint": "lintr", "Config/Needs/website": "BiocStyle, ggplot2, knitr, patchwork, pkgdown,\nragg, rmarkdown", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-30 13:20:38 UTC", "RemoteUrl": "https://github.com/bioc/pepVet", "RemoteRef": "HEAD", "RemoteSha": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 16:13:49 UTC", "User": "root" }, "Author": "Enes K. Ergin [aut, cre] (ORCID:\n)", "Maintainer": "Enes K. Ergin ", "_user": "bioc", "_type": "src", "_file": "pepVet_0.99.1.tar.gz", "_fileid": "https://r2.ropensci.org/405f99b8287e4827cc3b2ccccf7bc08274fd7ce45e392b64d0f887fa75886617", "_filesize": 1627724, "_sha256": "405f99b8287e4827cc3b2ccccf7bc08274fd7ce45e392b64d0f887fa75886617", "_expires": "2027-01-18T17:48:51.000Z", "_created": "2026-10-10T16:13:49.000Z", "_published": "2026-10-10T17:48:53.232Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 3 }, "_upstream": "https://github.com/bioc/pepVet", "_commit": { "id": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "author": "eneskemalergin ", "committer": "eneskemalergin ", "message": "chore: prepare 0.99.1 review revision\n", "time": 1785417638 }, "_maintainer": { "name": "Enes K. Ergin", "email": "eneskemalergin@gmail.com", "login": "eneskemalergin", "bluesky": "@eneskemalergin.bsky.social", "description": "Founder @Zenteomics & \nBioinformatician @LangeLab \n\nComputational Proteomics, Bioinformatics, Biostatistics, Systems Engineering", "uuid": 7672473, "orcid": "0000-0001-9810-7399" }, "_distro": "resolute", "_jobs": [ { "job": 114256108681, "time": 170, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11675129808" }, { "job": 114256108697, "time": 394, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11675525607" }, { "job": 114256108720, "time": 364, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11675264815" }, { "job": 114256108664, "time": 217, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11677670956" }, { "job": 114256108717, "time": 288, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11678250236" }, { "job": 114255437495, "time": 198, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11674929663" }, { "job": 114256108718, "time": 98, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11674449055" }, { "job": 114256108823, "time": 284, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11675014939" }, { "job": 114256108747, "time": 284, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11675144918" }, { "job": 114256108691, "time": 247, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11675515360" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "cleaver", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "ragg", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-12", "n": 8 }, { "week": "2026-13", "n": 11 }, { "week": "2026-18", "n": 3 }, { "week": "2026-20", "n": 12 }, { "week": "2026-21", "n": 26 }, { "week": "2026-25", "n": 9 }, { "week": "2026-26", "n": 2 }, { "week": "2026-28", "n": 30 }, { "week": "2026-29", "n": 18 }, { "week": "2026-31", "n": 7 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.1", "bioc": "3.24", "repository": "bioc" } ], "_topics": [ "proteomics", "massspectrometry", "qualitycontrol", "bioinformatics", "comparison", "digest", "enzyme", "quality-assurance" ], "_stars": 3, "_contributors": [ { "user": "eneskemalergin", "count": 126, "uuid": 7672473 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 212, "source": "https://www.bioconductor.org/packages/stats/bioc/pepVet" }, "_devurl": "https://github.com/langelab/pepvet", "_pkgdown": "https://langelab.github.io/pepVet/", "_searchresults": 12, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/pepVet.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/langelab/pepvet", "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotate_cleavage_sites", "batch_compare_enzymes", "batch_evaluate", "calculate_peptide_mass", "calculate_pI", "compare_digests", "digest_protein", "digest_report", "evaluate_digest", "export_peptide_list", "pepvet_check", "pepvet_plot_config", "pepvet_plot_config_reset", "pepvet_preset", "pepvet_save_figure", "pepvet_theme_manuscript", "pepvet_theme_presentation", "plot_batch_comparison", "plot_cleavage_map", "plot_coverage_map", "plot_digest_profile", "plot_enzyme_comparison", "plot_gravy_landscape", "plot_length_distribution", "plot_missed_cleavage_impact", "plot_mz_distribution", "plot_peptide_overlap_map", "plot_pI_distribution", "plot_proteome_overview", "plot_score_diagnostics", "plot_weight_sensitivity", "recommend_enzyme", "score_diagnostics", "score_peptides", "sensitivity_analysis", "summarize_batch", "triage_proteins" ], "_datasets": [ { "name": "aa_properties", "title": "Amino acid properties", "object": "aa_properties", "file": "aa_properties.rda", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "amino_acid", "molecular_weight", "residue_monoisotopic_mass", "hydrophobicity", "pKa_side_chain", "is_basic" ], "rows": 22, "table": true, "tojson": true } ], "_help": [ { "page": "aa_properties", "title": "Amino acid properties", "topics": [ "aa_properties" ] }, { "page": "annotate_cleavage_sites", "title": "Annotate cleavage-site efficiency", "concept": [ "digest" ], "topics": [ "annotate_cleavage_sites" ] }, { "page": "batch_compare_enzymes", "title": "Compare multiple enzymes across a full proteome", "concept": [ "evaluation" ], "topics": [ "batch_compare_enzymes" ] }, { "page": "batch_evaluate", "title": "Batch-evaluate multiple proteins", "concept": [ "evaluation" ], "topics": [ "batch_evaluate" ] }, { "page": "calculate_peptide_mass", "title": "Calculate peptide mass or m/z", "concept": [ "utils" ], "topics": [ "calculate_peptide_mass" ] }, { "page": "calculate_pI", "title": "Calculate peptide isoelectric point", "concept": [ "utils" ], "topics": [ "calculate_pI" ] }, { "page": "compare_digests", "title": "Compare multiple enzymes on a single protein", "concept": [ "evaluation" ], "topics": [ "compare_digests" ] }, { "page": "digest_protein", "title": "Simulate a proteolytic digest", "concept": [ "digest" ], "topics": [ "digest_protein" ] }, { "page": "digest_report", "title": "Print a compact console report for a proteolytic digest", "concept": [ "report" ], "topics": [ "digest_report" ] }, { "page": "evaluate_digest", "title": "Evaluate a proteolytic digest", "concept": [ "evaluation" ], "topics": [ "evaluate_digest" ] }, { "page": "export_peptide_list", "title": "Export a peptide list for downstream tools", "concept": [ "export" ], "topics": [ "export_peptide_list" ] }, { "page": "pepvet_check", "title": "Quick digest check for a single protein", "concept": [ "report" ], "topics": [ "pepvet_check" ] }, { "page": "pepvet_plot_config", "title": "Configure pepVet plot appearance", "concept": [ "plot-utils" ], "topics": [ "pepvet_plot_config" ] }, { "page": "pepvet_plot_config_reset", "title": "Reset pepVet plot configuration to defaults", "concept": [ "plot-utils" ], "topics": [ "pepvet_plot_config_reset" ] }, { "page": "pepvet_preset", "title": "Return a named scoring preset", "concept": [ "utils" ], "topics": [ "pepvet_preset" ] }, { "page": "pepvet_save_figure", "title": "Save a pepVet figure with publication-ready defaults", "concept": [ "plot-utils" ], "topics": [ "pepvet_save_figure" ] }, { "page": "pepvet_theme_manuscript", "title": "pepVet manuscript theme", "concept": [ "plot-utils" ], "topics": [ "pepvet_theme_manuscript" ] }, { "page": "pepvet_theme_presentation", "title": "pepVet presentation theme", "concept": [ "plot-utils" ], "topics": [ "pepvet_theme_presentation" ] }, { "page": "plot_batch_comparison", "title": "Multi-enzyme proteome comparison", "concept": [ "plot-batch" ], "topics": [ "plot_batch_comparison" ] }, { "page": "plot_cleavage_map", "title": "Cleavage Site Map", "concept": [ "plot-single" ], "topics": [ "plot_cleavage_map" ] }, { "page": "plot_coverage_map", "title": "Protein Coverage Map", "concept": [ "plot-single" ], "topics": [ "plot_coverage_map" ] }, { "page": "plot_digest_profile", "title": "Four-Panel Digest Diagnostic Plot", "concept": [ "plot-single" ], "topics": [ "plot_digest_profile" ] }, { "page": "plot_enzyme_comparison", "title": "Enzyme Comparison Chart", "concept": [ "plot-comparison" ], "topics": [ "plot_enzyme_comparison" ] }, { "page": "plot_gravy_landscape", "title": "GRAVY Landscape: 2D Scatter of Peptide Length vs. Hydrophobicity", "concept": [ "plot-distribution" ], "topics": [ "plot_gravy_landscape" ] }, { "page": "plot_length_distribution", "title": "Standalone Peptide Length Distribution", "concept": [ "plot-distribution" ], "topics": [ "plot_length_distribution" ] }, { "page": "plot_missed_cleavage_impact", "title": "Missed Cleavage Impact Plot", "concept": [ "plot-distribution" ], "topics": [ "plot_missed_cleavage_impact" ] }, { "page": "plot_mz_distribution", "title": "Precursor m/z Distribution", "concept": [ "plot-distribution" ], "topics": [ "plot_mz_distribution" ] }, { "page": "plot_peptide_overlap_map", "title": "Amino-Acid Peptide Overlap Map", "concept": [ "plot-single" ], "topics": [ "plot_peptide_overlap_map" ] }, { "page": "plot_pI_distribution", "title": "pI Distribution: Histogram of Peptide Isoelectric Points", "concept": [ "plot-distribution" ], "topics": [ "plot_pI_distribution" ] }, { "page": "plot_proteome_overview", "title": "Proteome digest overview", "concept": [ "plot-batch" ], "topics": [ "plot_proteome_overview" ] }, { "page": "plot_score_diagnostics", "title": "Plot score diagnostics", "concept": [ "diagnostics" ], "topics": [ "plot_score_diagnostics" ] }, { "page": "plot_weight_sensitivity", "title": "Plot weight sensitivity", "concept": [ "plot-single" ], "topics": [ "plot_weight_sensitivity" ] }, { "page": "recommend_enzyme", "title": "Return the highest-scoring enzyme for a single protein", "concept": [ "evaluation" ], "topics": [ "recommend_enzyme" ] }, { "page": "score_diagnostics", "title": "Score diagnostics for pepVet scoring models", "concept": [ "diagnostics" ], "topics": [ "score_diagnostics" ] }, { "page": "score_peptides", "title": "Score digested peptides for pre-acquisition review", "concept": [ "scoring" ], "topics": [ "score_peptides" ] }, { "page": "sensitivity_analysis", "title": "Weight sensitivity analysis", "concept": [ "evaluation" ], "topics": [ "sensitivity_analysis" ] }, { "page": "summarize_batch", "title": "Summarize a batch digest evaluation", "concept": [ "evaluation" ], "topics": [ "summarize_batch" ] }, { "page": "triage_proteins", "title": "Triage proteins from a batch evaluation", "concept": [ "evaluation" ], "topics": [ "triage_proteins" ] } ], "_pkglogo": "https://github.com/bioc/pepVet/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/pepVet/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "cleaver", "cli", "crayon", "generics", "glue", "IRanges", "lifecycle", "magrittr", "pillar", "pkgconfig", "rlang", "S4Vectors", "Seqinfo", "tibble", "utf8", "vctrs", "XVector" ], "_vignettes": [ { "source": "pepVet-introduction.Rmd", "filename": "pepVet-introduction.html", "title": "Getting Started with pepVet", "engine": "knitr::rmarkdown", "headings": [ "Installation", "The core pipeline", "Protein input", "Step 1: Digest a protein", "Step 1a: Inspect cleavage efficiency", "Step 2: Score the peptide set", "Scoring model", "Known limitations", "Scope", "Step 2a: Apply a workflow preset", "Step 2b: Add proteome-aware uniqueness", "Step 3: Evaluate in one call", "Step 4: Compare enzymes", "Step 5: Get the top model rank", "Step 6: Batch across a proteome", "Step 6a: Summarize a batch", "Step 6b: Triage proteins", "Step 6c: Export a peptide list", "Step 7: Quick interactive check", "Step 8: Report to the console", "Additional examples and references", "A challenging protein: Histone H3.1", "Amino acid reference data", "How pepVet differs from common tools", "Related articles", "Session info" ], "created": "2026-03-20 09:36:58", "modified": "2026-07-30 10:23:47", "commits": 27 }, { "source": "pepVet-tool-comparison.Rmd", "filename": "pepVet-tool-comparison.html", "title": "pepVet Compared to Other Tools", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Comparison basis", "Common ground", "How tools differ", "Worked comparisons", "pepVet scoring in practice", "Workflow preset effects", "Pipeline with PeptideRanger", "Binary versus graded: pepVet and Protein Cleaver", "Choosing an output type", "References", "Session info" ], "created": "2026-06-16 03:19:31", "modified": "2026-07-30 10:23:47", "commits": 11 } ], "_score": 5.556302500767288, "_indexed": true, "_nocasepkg": "pepvet", "_universes": [ "bioc", "eneskemalergin", "langelab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-10-10T16:17:42.000Z", "distro": "resolute", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/eb641b57775f39ec380d8ae5c9e40a11ed7667da2fa51ab54273d17e8b3e28b4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.6.1", "os": "linux", "version": "0.99.1", "date": "2026-10-10T16:17:33.000Z", "distro": "resolute", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/fab5a6fc835a3470102982d5e6e0c6fa78aecb83c7e55f53bca1047dd1d99932", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-10-10T17:39:50.000Z", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/ef81ed384d0c6971064d787f6f95f5b33472be9d9e62f58ae2bb7481ac3fb552", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.6.1", "os": "mac", "version": "0.99.1", "date": "2026-10-10T17:45:27.000Z", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/d659771aaea87c3349355562d000fa875e4067e6ff37e43e61bc492d8e302fe3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.1", "date": "2026-10-10T16:15:57.000Z", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/3209d8d6daf37e5a916ced021a23fa881bdd6f8bca0dd1983397d382d23ccb3a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-10-10T16:15:39.000Z", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/29107bc3cce8bef3ecce3646a96a0e5e4000daeef38ad5ee851a8aed4b9ec4b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.5.3", "os": "win", "version": "0.99.1", "date": "2026-10-10T16:15:14.000Z", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/aee1a065dafee3435cf04833ff7445a340bf112a6a43a763a6961253f9938a96", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" }, { "r": "4.6.1", "os": "win", "version": "0.99.1", "date": "2026-10-10T16:15:02.000Z", "commit": "6582caf217e1cc8c0e44de2dd4e502d1e19febad", "fileid": "https://r2.ropensci.org/a1a0ece5bd6ab522ba6831388f8f365a903112cb51ab6c2e784237ad4fc63fc9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38066593434" } ] }