{
  "_id": "6a5f219a14e95619b75d44b6",
  "Package": "signalHsmm",
  "Type": "Package",
  "Title": "Predict Presence of Signal Peptides",
  "Version": "1.5",
  "LazyData": "true",
  "Date": "2018-11-11",
  "Authors@R": "c(person(\"Michal\", \"Burdukiewicz\", \nemail = \"michalburdukiewicz@gmail.com\",\nrole = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0001-8926-582X\")),\nperson(\"Piotr\", \"Sobczyk\", email = \"sobbombo@gmail.com\", role = \"aut\"),\nperson(\"Jaroslaw\", \"Chilimoniuk\",\nemail = \"jaroslaw.chilimoniuk@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5467-018X\"),\nrole = c(\"ctb\")))",
  "Description": "Predicts the presence of signal peptides in eukaryotic\nprotein using hidden semi-Markov models. The implemented\nalgorithm can be accessed from both the command line and GUI.",
  "License": "GPL-3",
  "URL": "https://github.com/michbur/signalhsmm",
  "NeedsCompilation": "yes",
  "Encoding": "UTF-8",
  "RoxygenNote": "6.1.0",
  "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev",
  "Repository": "https://michbur.r-universe.dev",
  "Date/Publication": "2020-05-04 14:03:28 UTC",
  "RemoteUrl": "https://github.com/michbur/signalhsmm",
  "RemoteRef": "HEAD",
  "RemoteSha": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
  "Packaged": {
    "Date": "2026-07-21 07:32:06 UTC",
    "User": "root"
  },
  "Author": "Michal Burdukiewicz [cre, aut] (ORCID:\n<https://orcid.org/0000-0001-8926-582X>),\nPiotr Sobczyk [aut],\nJaroslaw Chilimoniuk [ctb] (ORCID:\n<https://orcid.org/0000-0001-5467-018X>)",
  "Maintainer": "Michal Burdukiewicz <michalburdukiewicz@gmail.com>",
  "_user": "michbur",
  "_type": "src",
  "_file": "signalHsmm_1.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/7305636ce077e88ad04e592c76e3de72bb839eaff2f187244b71145036d02516",
  "_filesize": 193706,
  "_sha256": "7305636ce077e88ad04e592c76e3de72bb839eaff2f187244b71145036d02516",
  "_expires": "2026-10-29T07:36:56.000Z",
  "_created": "2026-07-21T07:32:06.000Z",
  "_published": "2026-07-21T07:36:58.411Z",
  "_jobs": [
    {
      "job": 88571198569,
      "time": 139,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8487380544"
    },
    {
      "job": 88571198548,
      "time": 134,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8487377608"
    },
    {
      "job": 88571198500,
      "time": 136,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8487379520"
    },
    {
      "job": 88571198522,
      "time": 129,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8487375395"
    },
    {
      "job": 88571198636,
      "time": 127,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8487368790"
    },
    {
      "job": 88571198604,
      "time": 246,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8487413871"
    },
    {
      "job": 88571199043,
      "time": 161,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8487376325"
    },
    {
      "job": 88571198665,
      "time": 209,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8487401151"
    },
    {
      "job": 88570578186,
      "time": 190,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8487323769"
    },
    {
      "job": 88571198467,
      "time": 123,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8487372363"
    },
    {
      "job": 88571198564,
      "time": 118,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8487371624"
    },
    {
      "job": 88571198570,
      "time": 101,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8487364237"
    },
    {
      "job": 88571198553,
      "time": 100,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8487363863"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468",
  "_status": "success",
  "_upstream": "https://github.com/michbur/signalhsmm",
  "_commit": {
    "id": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
    "author": "jarochi <jaroslaw.chilimoniuk@gmail.com>",
    "committer": "jarochi <jaroslaw.chilimoniuk@gmail.com>",
    "message": "services:\n - xvfb\n",
    "time": 1588601008
  },
  "_maintainer": {
    "name": "Michal Burdukiewicz",
    "email": "michalburdukiewicz@gmail.com",
    "login": "michbur",
    "bluesky": "@burdukiewicz.bsky.social",
    "orcid": "0000-0001-8926-582X",
    "twitter": "@burdukiewicz",
    "description": "",
    "uuid": 5267317
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "shinythemes",
      "role": "Suggests"
    }
  ],
  "_owner": "michbur",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "michbur",
      "count": 161,
      "uuid": 5267317
    },
    {
      "user": "psobczyk",
      "count": 19,
      "uuid": 1227394
    },
    {
      "user": "jarochi",
      "count": 10,
      "uuid": 33185176
    },
    {
      "user": "ironholds",
      "count": 1,
      "uuid": 2487262
    }
  ],
  "_userbio": {
    "uuid": 5267317,
    "type": "user",
    "name": "Michał Burdukiewicz",
    "followers": 114
  },
  "_downloads": {
    "count": 253,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/signalHsmm"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/michbur/signalhsmm",
  "_searchresults": 9,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/signalHsmm.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/michbur/signalhsmm",
  "_realowner": "michbur",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.3",
      "date": "2015-07-03"
    },
    {
      "version": "1.4",
      "date": "2016-03-03"
    },
    {
      "version": "1.5",
      "date": "2018-11-15"
    }
  ],
  "_exports": [
    "add_k_mer_state",
    "duration_viterbi",
    "find_nhc",
    "gui_signalHsmm",
    "is_protein",
    "pred2df",
    "read_txt",
    "read_uniprot",
    "run_signalHsmm",
    "train_hsmm"
  ],
  "_datasets": [
    {
      "name": "aaaggregation",
      "title": "Reduced amino acid alphabet",
      "object": "aaaggregation",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "benchmark_dat",
      "title": "Benchmark data set for signalHsmm",
      "object": "benchmark_dat",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aaaggregation",
      "title": "Reduced amino acid alphabet",
      "topics": [
        "aaaggregation"
      ]
    },
    {
      "page": "add_k_mer_state",
      "title": "Adds k-mer hidden state to signalHsmm model",
      "topics": [
        "add_k_mer_state"
      ]
    },
    {
      "page": "benchmark_dat",
      "title": "Benchmark data set for signalHsmm",
      "topics": [
        "benchmark_dat"
      ]
    },
    {
      "page": "duration_viterbi",
      "title": "Compute most probable path with extended Viterbi algorithm.",
      "topics": [
        "duration_viterbi"
      ]
    },
    {
      "page": "find_nhc",
      "title": "Localize n-, h- and c-region in signal peptide",
      "topics": [
        "find_nhc"
      ]
    },
    {
      "page": "gui_signalHsmm",
      "title": "GUI for signalHsmm",
      "topics": [
        "gui_signalHsmm"
      ]
    },
    {
      "page": "hsmm_pred",
      "title": "hsmm_pred class",
      "topics": [
        "hsmm_pred"
      ]
    },
    {
      "page": "hsmm_pred_list",
      "title": "hsmm_pred_list class",
      "topics": [
        "hsmm_pred_list"
      ]
    },
    {
      "page": "is_protein",
      "title": "Protein test",
      "topics": [
        "is_protein"
      ]
    },
    {
      "page": "plot.hsmm_pred",
      "title": "Plot single signalHsmm prediction",
      "topics": [
        "plot.hsmm_pred"
      ]
    },
    {
      "page": "pred2df",
      "title": "Convert list of signalHsmm predictions",
      "topics": [
        "pred2df"
      ]
    },
    {
      "page": "predict.sighsmm_model",
      "title": "Predict sighsmm_model object",
      "topics": [
        "predict.sighsmm_model"
      ]
    },
    {
      "page": "read_txt",
      "title": "Read sequences from .txt file",
      "topics": [
        "read_txt"
      ]
    },
    {
      "page": "read_uniprot",
      "title": "Read data from UniProt database",
      "topics": [
        "read_uniprot"
      ]
    },
    {
      "page": "run_signalHsmm",
      "title": "Predict presence of signal peptide in protein",
      "topics": [
        "run_signalHsmm"
      ]
    },
    {
      "page": "signalHsmm",
      "title": "signalHsmm - prediction of signal peptides",
      "topics": [
        "signalHsmm-package",
        "signalHsmm"
      ]
    },
    {
      "page": "summary.hsmm_pred",
      "title": "Summarize single signalHsmm prediction",
      "topics": [
        "summary.hsmm_pred"
      ]
    },
    {
      "page": "summary.hsmm_pred_list",
      "title": "Summarize list of signalHsmm predictions",
      "topics": [
        "summary.hsmm_pred_list"
      ]
    },
    {
      "page": "train_hsmm",
      "title": "Train sighsmm_model object",
      "topics": [
        "train_hsmm"
      ]
    }
  ],
  "_readme": "https://github.com/michbur/signalhsmm/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "digest",
    "fastmap",
    "fontawesome",
    "fs",
    "glue",
    "htmltools",
    "httpuv",
    "jquerylib",
    "jsonlite",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "memoise",
    "mime",
    "nlme",
    "otel",
    "pixmap",
    "promises",
    "R6",
    "rappdirs",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "sass",
    "segmented",
    "seqinr",
    "shiny",
    "sourcetools",
    "sp",
    "withr",
    "xtable"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "signalhsmm",
  "_universes": [
    "michbur"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5",
      "date": "2026-07-21T07:34:31.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/95f07e32b35eda5607747961c18e0e1046124524e3f8a5a7dabcb3c4f35b69f8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5",
      "date": "2026-07-21T07:34:19.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/f97fb71736550805082e3d2c24a00385dcb5c73f55d4829d4bbc9e2190ecb745",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5",
      "date": "2026-07-21T07:34:29.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/76baef7a72e908d7e2c4e61c0a32e392793b63b7100a3ceaccecfddd17014a6b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5",
      "date": "2026-07-21T07:34:16.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/805625af9857dab9ac8d3352e85d665f6b3cd87423afde6350a0aebf857f5de6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5",
      "date": "2026-07-21T07:34:02.000Z",
      "arch": "aarch64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/82dc242f77771bbbb44b656bb9d9341023c14952fe74a16c4657661a8bdb5f7b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5",
      "date": "2026-07-21T07:35:34.000Z",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/3c4a3ad4d6fdbfe117f9763693f19c328d4873e78d4cbedd48f63ff0f4269364",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5",
      "date": "2026-07-21T07:34:16.000Z",
      "arch": "aarch64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/dc2ed9c79d083de258a42019c83514ac326c0173fdb05a99622ad61d4d1a4320",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5",
      "date": "2026-07-21T07:35:04.000Z",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/77975215be480d51760a11aaa80d58bdf80d5ff8ed57b5f63eecdb5151fcdbfe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5",
      "date": "2026-07-21T07:34:23.000Z",
      "arch": "emscripten",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/e14633c79529f4c889ae22dd7d00931052868250892b7aaebbf5ef3e0f04479e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5",
      "date": "2026-07-21T07:33:39.000Z",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/7cc4858020c601bce9c772cd15e4bd1ab715a2f5ad427e47399bf3de20695160",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5",
      "date": "2026-07-21T07:33:22.000Z",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/f45ce990bf2d200582f40a96ea9fff2fe258ab0f5a0e4dc8cdabe2d11a3dd674",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.5",
      "date": "2026-07-21T07:33:21.000Z",
      "arch": "x86_64",
      "commit": "7a9a3a72362eeb0cca5db0e51f33ec26508b5af1",
      "fileid": "https://r2.ropensci.org/a48e33aeb17c93ad35bc35e3d5864d4c85f1f13619b328a49c7f8ce876dca6b7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/michbur/actions/runs/29810599468"
    }
  ]
}