{
  "_id": "6a102d59acfb0bcc41c93a64",
  "Package": "LncFinder",
  "Type": "Package",
  "Title": "LncRNA Identification and Analysis Using Heterologous Features",
  "Version": "1.1.6",
  "Authors@R": "c(\nperson(family = \"Han\", given = \"Siyu\", email = \"siyu.han@tum.de\", role = c(\"aut\", \"cre\")),\nperson(family = \"Li\", given = \"Ying\", email = \"liying@jlu.edu.cn\", role = \"aut\"),\nperson(family = \"Liang\", given = \"Yanchun\", role = \"aut\"))",
  "Maintainer": "Siyu Han <siyu.han@tum.de>",
  "Acknowledgments": "CHENG Ming, FAN Linrui, GUO Yuan, LI Yaolong, SUN\nYing, WANG Ruoyu",
  "Description": "Long non-coding RNAs identification and analysis. Default\nmodels are trained with human, mouse and wheat datasets by\nemploying SVM. Features are based on intrinsic composition of\nsequence, EIIP value (electron-ion interaction\npseudopotential), and secondary structure. This package can\nalso extract other classic features and build new classifiers.\nReference: Han S., et al. (2019) <doi:10.1093/bib/bby065>.",
  "URL": "https://lncfinder.osubmi.org/",
  "License": "GPL-3",
  "LazyData": "true",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "NeedsCompilation": "no",
  "Author": "Siyu Han [aut, cre], Ying Li [aut], Yanchun Liang [aut]",
  "Packaged": {
    "Date": "2026-05-13 05:49:59 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://han-siyu.r-universe.dev",
  "Date/Publication": "2024-09-29 03:04:26 UTC",
  "RemoteUrl": "https://github.com/cran/LncFinder",
  "RemoteRef": "HEAD",
  "RemoteSha": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
  "MD5sum": "e43dbd11a21b0ea96aabb0fba59c26e4",
  "_user": "han-siyu",
  "_type": "src",
  "_file": "LncFinder_1.1.6.tar.gz",
  "_fileid": "8d9f50c9f24fa0a2babac7237341584aefafde266de5463144f263a9e411aed1",
  "_filesize": 2486759,
  "_sha256": "8d9f50c9f24fa0a2babac7237341584aefafde266de5463144f263a9e411aed1",
  "_created": "2026-05-13T05:49:59.000Z",
  "_published": "2026-05-22T10:18:01.049Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77360216731,
      "time": 181,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6962607760"
    },
    {
      "job": 77360216755,
      "time": 159,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6962602670"
    },
    {
      "job": 77360216691,
      "time": 192,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6962600646"
    },
    {
      "job": 77360216540,
      "time": 247,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6962609839"
    },
    {
      "job": 77360216278,
      "time": 188,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6962565959"
    },
    {
      "job": 77360216028,
      "time": 111,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158163251"
    },
    {
      "job": 77360216632,
      "time": 130,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6962596232"
    },
    {
      "job": 77360216921,
      "time": 117,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6962593258"
    },
    {
      "job": 77360216463,
      "time": 135,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6962597920"
    }
  ],
  "_buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/LncFinder",
  "_commit": {
    "id": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
    "author": "Siyu Han <siyu.han@tum.de>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.1.6\n",
    "time": 1727579066
  },
  "_maintainer": {
    "name": "Siyu Han",
    "email": "siyu.han@tum.de",
    "login": "han-siyu",
    "linkedin": "in/han-siyu",
    "uuid": 16144249
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "seqinr",
      "version": ">= 2.1-3",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "version": ">= 2.1.0",
      "role": "Imports"
    },
    {
      "package": "caret",
      "version": ">= 6.0-71",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "han-siyu",
      "count": 5,
      "uuid": 16144249
    }
  ],
  "_userbio": {
    "uuid": 16144249,
    "type": "user",
    "name": "Han, Siyu",
    "description": "Computational Health Center, Helmholtz Munich - German Research Center for Environmental Health"
  },
  "_downloads": {
    "count": 423,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/LncFinder"
  },
  "_mentions": 9,
  "_searchresults": 61,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/LncFinder.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "han-siyu",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2017-02-06"
    },
    {
      "version": "1.1.3",
      "date": "2018-08-02"
    },
    {
      "version": "1.1.4",
      "date": "2020-07-01"
    },
    {
      "version": "1.1.5",
      "date": "2021-12-09"
    },
    {
      "version": "1.1.6",
      "date": "2024-09-28"
    }
  ],
  "_exports": [
    "build_model",
    "compute_EIIP",
    "compute_EucDistance",
    "compute_FickettScore",
    "compute_GC",
    "compute_hexamerScore",
    "compute_kmer",
    "compute_LogDistance",
    "compute_pI",
    "extract_features",
    "find_orfs",
    "lnc_finder",
    "make_frequencies",
    "make_referFreq",
    "read_SS",
    "run_RNAfold",
    "svm_cv",
    "svm_tune"
  ],
  "_datasets": [
    {
      "name": "demo_dataset",
      "title": "A demo of dataset",
      "object": "demo_dataset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Label",
        "ORF.Max.Len",
        "ORF.Max.Cov",
        "Seq.lnc.Dist",
        "Seq.pct.Dist",
        "Seq.Dist.Ratio",
        "Signal.Peak",
        "SNR",
        "Signal.Min",
        "Signal.Q1",
        "Signal.Q2",
        "Signal.Max",
        "Dot_lnc.dist",
        "Dot_pct.dist",
        "Dot_Dist.Ratio",
        "SS.lnc.dist",
        "SS.pct.dist",
        "SS.Dist.Ratio",
        "MFE",
        "UP.PCT"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "demo_DNA.seq",
      "title": "A demo of DNA sequences",
      "object": "demo_DNA.seq",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "demo_SS.seq",
      "title": "A demo of secondary structure sequences",
      "object": "demo_SS.seq",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ENST00000510062.1",
        "ENST00000515405.1",
        "ENST00000509096.1",
        "ENST00000508985.1",
        "ENST00000510225.1",
        "ENST00000508313.1",
        "ENST00000509956.1",
        "ENST00000515840.1",
        "ENST00000503929.1",
        "ENST00000512241.1"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "build_model",
      "title": "Build Users' Own Model",
      "topics": [
        "build_model"
      ]
    },
    {
      "page": "compute_EIIP",
      "title": "Extract the EIIP-derived features",
      "topics": [
        "compute_EIIP"
      ]
    },
    {
      "page": "compute_EucDistance",
      "title": "Compute Euclidean Distance",
      "topics": [
        "compute_EucDistance"
      ]
    },
    {
      "page": "compute_FickettScore",
      "title": "Compute Fickett TESTCODE Score",
      "topics": [
        "compute_FickettScore"
      ]
    },
    {
      "page": "compute_GC",
      "title": "Calculate GC content",
      "topics": [
        "compute_GC"
      ]
    },
    {
      "page": "compute_hexamerScore",
      "title": "Compute Hexamer Score",
      "topics": [
        "compute_hexamerScore"
      ]
    },
    {
      "page": "compute_kmer",
      "title": "Compute _k_-mer Features",
      "topics": [
        "compute_kmer"
      ]
    },
    {
      "page": "compute_LogDistance",
      "title": "Compute Logarithm Distance",
      "topics": [
        "compute_LogDistance"
      ]
    },
    {
      "page": "compute_pI",
      "title": "Compute Theoretical Isoelectric Point",
      "topics": [
        "compute_pI"
      ]
    },
    {
      "page": "demo_dataset",
      "title": "A demo of dataset",
      "topics": [
        "demo_dataset"
      ]
    },
    {
      "page": "demo_DNA.seq",
      "title": "A demo of DNA sequences",
      "topics": [
        "demo_DNA.seq"
      ]
    },
    {
      "page": "demo_SS.seq",
      "title": "A demo of secondary structure sequences",
      "topics": [
        "demo_SS.seq"
      ]
    },
    {
      "page": "extract_features",
      "title": "Extract the Features",
      "topics": [
        "extract_features"
      ]
    },
    {
      "page": "find_orfs",
      "title": "Find ORFs",
      "topics": [
        "find_orfs"
      ]
    },
    {
      "page": "lnc_finder",
      "title": "Long Non-coding RNA Identification",
      "topics": [
        "lnc_finder"
      ]
    },
    {
      "page": "make_frequencies",
      "title": "Make the frequencies file for new classifier construction",
      "topics": [
        "make_frequencies"
      ]
    },
    {
      "page": "make_referFreq",
      "title": "Make Frequencies File for Log.Dist, Euc.Dist, and hexamer score",
      "topics": [
        "make_referFreq"
      ]
    },
    {
      "page": "read_SS",
      "title": "Read Secondary Structure Information",
      "topics": [
        "read_SS"
      ]
    },
    {
      "page": "run_RNAfold",
      "title": "Obtain the Secondary Structure Sequences Using RNAfold",
      "topics": [
        "run_RNAfold"
      ]
    },
    {
      "page": "svm_cv",
      "title": "_k_-fold Cross Validation for SVM",
      "topics": [
        "svm_cv"
      ]
    },
    {
      "page": "svm_tune",
      "title": "Parameter Tuning of SVM",
      "topics": [
        "svm_tune"
      ]
    }
  ],
  "_readme": "https://github.com/cran/LncFinder/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "caret",
    "class",
    "cli",
    "clock",
    "codetools",
    "cpp11",
    "data.table",
    "diagram",
    "digest",
    "dplyr",
    "e1071",
    "farver",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "ipred",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "ModelMetrics",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "pillar",
    "pixmap",
    "pkgconfig",
    "plyr",
    "pROC",
    "prodlim",
    "progressr",
    "proxy",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "recipes",
    "reshape2",
    "rlang",
    "rpart",
    "S7",
    "scales",
    "segmented",
    "seqinr",
    "shape",
    "sp",
    "sparsevctrs",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 3.739572344450092,
  "_indexed": true,
  "_nocasepkg": "lncfinder",
  "_universes": [
    "han-siyu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.6",
      "date": "2026-05-13T05:52:30.000Z",
      "distro": "noble",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "8dae5b34aa437aec00cca3de5d0f3a8fd1861662d304c84d61b464ec68df82cc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.6",
      "date": "2026-05-13T05:52:13.000Z",
      "distro": "noble",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "f33b9a71d4d3f84da8af3a8b88654abc810d09fd733dd5d30dab73c1ef2087d1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.6",
      "date": "2026-05-13T05:52:12.000Z",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "c73393d0085ba66ba5444e1a283b5c417ae89aa7431f72cb37fb88684cc13cd2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.6",
      "date": "2026-05-13T05:52:42.000Z",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "ac61459811b5498dc0f4f55c5311bff4acb337bf57a1d98360bf590458eff5c8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.6",
      "date": "2026-05-13T05:51:34.000Z",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "6fff39ec3e88e59f77093551b5d4e70bbfdb9b5a42a54d1e93b439d05a521b0a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.6",
      "date": "2026-05-13T05:51:22.000Z",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "6c86518ba658a4754ad0f56299eb3e02f4c2488501c26f0b001cd67f8aa48c1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.6",
      "date": "2026-05-13T05:51:44.000Z",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "1fa6dca4aeb6faed35dec1991f52e296b3261c687db2e3c54d18f613afc549c8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.6",
      "date": "2026-05-22T10:17:33.000Z",
      "commit": "fbef81fcc6992617d2cb753fc51c8ae2320a3876",
      "fileid": "f8158df50e12c630fc59010b40498b239775f8a45c110fbf507b9cc7b76bd7ba",
      "status": "success",
      "buildurl": "https://github.com/r-universe/han-siyu/actions/runs/25780922793"
    }
  ]
}