{ "_id": "6aae46893d719c1f8407a8ab", "Package": "tailor", "Type": "Package", "Title": "Tool for Adapter-domain Identification and Linking Of RBPs", "Version": "0.1.1", "Authors@R": "c(\nperson(\"András\", \"Asbóth\", role = c(\"aut\", \"cre\"),\nemail = \"sbthandras+bioinfo@gmail.com\",\ncomment = c(ORCID = \"0009-0001-2284-412X\")),\nperson(\"Tamás\", \"Stirling\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8964-6443\")))", "Description": "Bacteriophages (phages) are viruses that infect bacteria.\nMany phages encode receptor binding proteins (RBPs) that\nmediate attachment to their bacterial hosts. Most RBPs contain\na conserved N-terminal domain (we refer to this as an\n\"adapter\") which anchors the protein to the phage particle.\nThis package provides functions to indentify these adapters and\ngroup them based on sequence similarity.", "Remotes": [ "stitam/breakpoint" ], "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0.9000", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://stitam.r-universe.dev", "Date/Publication": "2026-06-21 11:17:24 UTC", "RemoteUrl": "https://github.com/sbthandras/tailor", "RemoteRef": "HEAD", "RemoteSha": "93f99d3534c96514a358c4862bd0031101efc848", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-19 08:19:28 UTC", "User": "root" }, "Author": "András Asbóth [aut, cre] (ORCID:\n),\nTamás Stirling [aut] (ORCID: )", "Maintainer": "András Asbóth ", "_user": "stitam", "_type": "src", "_file": "tailor_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/1295adffe29cfd3f81006ec8c37a94bb0316d536f1d04ad523d368fd12ff2264", "_filesize": 2077838, "_sha256": "1295adffe29cfd3f81006ec8c37a94bb0316d536f1d04ad523d368fd12ff2264", "_expires": "2026-12-28T08:23:35.000Z", "_created": "2026-09-19T08:19:28.000Z", "_published": "2026-09-19T08:23:36.976Z", "_jobs": [ { "job": 105867360505, "time": 196, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10580753815" }, { "job": 105867360566, "time": 195, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10580144579" }, { "job": 105867360520, "time": 137, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10580503943" }, { "job": 105867360490, "time": 130, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10580388889" }, { "job": 105866969278, "time": 197, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10580503796" }, { "job": 105867360504, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10580858494" }, { "job": 105867360572, "time": 154, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10580454007" }, { "job": 105867360634, "time": 138, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10580853566" }, { "job": 105867360588, "time": 135, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10581028205" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190", "_status": "success", "_upstream": "https://github.com/sbthandras/tailor", "_commit": { "id": "93f99d3534c96514a358c4862bd0031101efc848", "author": "Tamás Stirling <49147718+stitam@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #11 from sbthandras/adapter_matrix\n\nAllow more variables for constructing the adapter matrix and improve plotting", "time": 1782040644 }, "_maintainer": { "name": "András Asbóth", "email": "sbthandras+bioinfo@gmail.com", "login": "huuuuuuuuuuu", "description": "", "uuid": 48626801, "orcid": "0009-0001-2284-412X" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "breakpoint", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "qcc", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" } ], "_owner": "sbthandras", "_selfowned": false, "_usedby": 51, "_updates": [ { "week": "2026-09", "n": 1 }, { "week": "2026-10", "n": 7 }, { "week": "2026-24", "n": 2 }, { "week": "2026-25", "n": 3 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-03-02" }, { "name": "v1.0.0", "date": "2026-03-03" } ], "_stars": 3, "_contributors": [ { "user": "stitam", "count": 73, "uuid": 49147718 }, { "user": "sbthandras", "count": 1, "uuid": 86297087 } ], "_userbio": { "uuid": 49147718, "type": "user", "name": "Tamás Stirling", "followers": 28 }, "_downloads": { "count": 22300, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tailor" }, "_devurl": "https://github.com/sbthandras/tailor", "_searchresults": 42, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/tailor.html" ], "_homeurl": "https://github.com/tidymodels/tailor", "_realowner": "tidymodels", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2025-08-25" } ], "_exports": [ "adapter_matrix", "cluster_adapters", "completeness", "filter_comparisons", "find_adapter", "find_all_adapters", "find_breakpoints", "homogeneity", "position_scores", "schoco", "validate_rbps" ], "_datasets": [ { "name": "adapters", "title": "Adapters", "object": "adapters", "class": [ "adapter", "data.frame" ], "fields": [ "pattern_id", "subject_id", "start", "end", "mean_score", "pident" ], "rows": 190, "table": true, "tojson": true }, { "name": "rbps", "title": "Receptor Binding Proteins", "object": "rbps", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Core_ORF", "translation" ], "rows": 20, "table": true, "tojson": true } ], "_help": [ { "page": "adapter_matrix", "title": "Create adapter matrix", "topics": [ "adapter_matrix" ] }, { "page": "adapters", "title": "Adapters", "topics": [ "adapters" ] }, { "page": "cluster_adapters", "title": "Group RBPs into adapter clusters", "topics": [ "cluster_adapters" ] }, { "page": "completeness", "title": "Completeness", "topics": [ "completeness" ] }, { "page": "filter_comparisons", "title": "Filter comparisons", "topics": [ "filter_comparisons" ] }, { "page": "find_adapter", "title": "Find adapter region", "topics": [ "find_adapter" ] }, { "page": "find_all_adapters", "title": "Find all adapters for a set of RBPs", "topics": [ "find_all_adapters" ] }, { "page": "find_breakpoints", "title": "Find breakpoints in global alignment scores", "topics": [ "find_breakpoints", "find_breakpoints_cemean", "find_breakpoints_plateau", "find_breakpoints_window" ] }, { "page": "homogeneity", "title": "Homogeneity", "topics": [ "homogeneity" ] }, { "page": "plot.adapter_matrix", "title": "Plot adapter matrix", "topics": [ "plot.adapter_matrix" ] }, { "page": "plot.ps", "title": "Plot pairwise alignment scores with adapter regions", "topics": [ "plot.ps" ] }, { "page": "position_scores", "title": "Pairwise global alignments with position scores", "topics": [ "position_scores" ] }, { "page": "rbps", "title": "Receptor Binding Proteins", "topics": [ "rbps" ] }, { "page": "schoco", "title": "SCores of HOmogeneity and COmpleteness", "topics": [ "schoco" ] }, { "page": "validate_rbps", "title": "Validate RBP data set", "topics": [ "validate_rbps" ] } ], "_readme": "https://github.com/sbthandras/tailor/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "breakpoint", "cli", "codetools", "cpp11", "crayon", "doParallel", "dplyr", "expm", "farver", "foreach", "generics", "ggplot2", "glue", "gtable", "IRanges", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "msm", "mvtnorm", "patchwork", "pillar", "pkgconfig", "plyr", "purrr", "pwalign", "qcc", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_score": 6.934396834647304, "_indexed": false, "_nocasepkg": "tailor", "_universes": [ "stitam" ], "_indexurl": "https://tidymodels.r-universe.dev/tailor", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-09-19T08:21:43.000Z", "distro": "resolute", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/8a0e8c1c17cc9878824ea6d22b510685ef61ca95616a9f6ed5caded15865abbd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.6.1", "os": "linux", "version": "0.1.1", "date": "2026-09-19T08:21:44.000Z", "distro": "resolute", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/3d8bf30f32cb4f6fb0a614e0a8b7880f405807c532fa875e032e45c4a59b28d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.5.3", "os": "mac", "version": "0.1.1", "date": "2026-09-19T08:21:16.000Z", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/41ff45c127bc7251f18d43094dcb2a0e068151535b70d6c3d2a6223506640119", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.6.1", "os": "mac", "version": "0.1.1", "date": "2026-09-19T08:21:05.000Z", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/bc4800e85132f9771da502998e15abd7b4d1349350b1d0a071b6a31aa049cf5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-09-19T08:22:00.000Z", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/a06b9096df22eea8580195d0a51c55cfd12852194445a0d8168ec1a1e093a8b1", "status": "success", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-09-19T08:20:42.000Z", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/6077344058829807c40754bbce9dc28150a51c76d05276a84a4e4c39db20a0ac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.5.3", "os": "win", "version": "0.1.1", "date": "2026-09-19T08:20:33.000Z", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/d35c29fa7f6000f5ec455ba36857f7fa8fa8265e1a8c14e979de493aaa235faf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" }, { "r": "4.6.1", "os": "win", "version": "0.1.1", "date": "2026-09-19T08:20:45.000Z", "commit": "93f99d3534c96514a358c4862bd0031101efc848", "fileid": "https://r2.ropensci.org/ddf5e772ac766799c2cd7c5bdcaec9bd95b4c13a1275ed8257347c679ae74bb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stitam/actions/runs/35431538190" } ] }