{ "_id": "6a103727acfb0bcc41c9a3b5", "Package": "netmhc2pan", "Title": "Interface to 'NetMHCIIpan'", "Version": "1.3.3", "Authors@R": "c(\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"rjcbilderbeek@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1107-7049\")),\nperson(\"Lue Ping\", \"Zhao\", role = \"ctb\"),\nperson(\"Byungkuk\", \"Min\", role = \"ctb\"))", "Maintainer": "Richèl J.C. Bilderbeek ", "Description": "The field of immunology benefits from software that can\npredict which peptide sequences trigger an immune response.\n'NetMHCIIpan' is a such a tool: it predicts the binding\nstrength of a short peptide to a Major Histocompatibility\nComplex class II (MHC-II) molecule. 'NetMHCIIpan' can be used\nfrom a web server at\n\nor from the command-line, using a local installation. This\npackage allows to call 'NetMHCIIpan' from R.", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.3", "Language": "en-US", "URL": "https://github.com/richelbilderbeek/netmhc2pan/", "BugReports": "https://github.com/richelbilderbeek/netmhc2pan/issues", "SystemRequirements": "NetMHC2pan\n(https://services.healthtech.dtu.dk/service.php?NetMHCIIpan-3.2)", "Config/pak/sysreqs": "libicu-dev libx11-dev zlib1g-dev", "Repository": "https://richelbilderbeek.r-universe.dev", "Date/Publication": "2024-07-10 14:27:46 UTC", "RemoteUrl": "https://github.com/richelbilderbeek/netmhc2pan", "RemoteRef": "HEAD", "RemoteSha": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 06:32:32 UTC", "User": "root" }, "Author": "Richèl J.C. Bilderbeek [aut, cre] (ORCID:\n),\nLue Ping Zhao [ctb],\nByungkuk Min [ctb]", "MD5sum": "bc09f6680cb8408acd30f96ebf92f931", "_user": "richelbilderbeek", "_type": "src", "_file": "netmhc2pan_1.3.3.tar.gz", "_fileid": "c4abb53ceff7d0219ed363fe7119410f556f593773346109607787d687bffa14", "_filesize": 210155, "_sha256": "c4abb53ceff7d0219ed363fe7119410f556f593773346109607787d687bffa14", "_created": "2026-05-12T06:32:32.000Z", "_published": "2026-05-22T10:59:51.605Z", "_distro": "noble", "_jobs": [ { "job": 77366271987, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "6937280900" }, { "job": 77366271858, "time": 134, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "6937279179" }, { "job": 77366271733, "time": 105, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6937271988" }, { "job": 77366271688, "time": 96, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6937269870" }, { "job": 77366271464, "time": 200, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6937245749" }, { "job": 77366271120, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158883743" }, { "job": 77366271576, "time": 108, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "6937272919" }, { "job": 77366271671, "time": 96, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "6937270104" }, { "job": 77366271739, "time": 84, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "6937267088" } ], "_buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/richelbilderbeek/netmhc2pan", "_commit": { "id": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "author": "richelbilderbeek ", "committer": "richelbilderbeek ", "message": "Merge branch 'master' into develop\n", "time": 1720621666 }, "_maintainer": { "name": "Richèl J.C. Bilderbeek", "email": "rjcbilderbeek@gmail.com", "login": "richelbilderbeek", "orcid": "0000-0003-1107-7049", "uuid": 2098230 }, "_registered": true, "_dependencies": [ { "package": "dplyr", "role": "Imports" }, { "package": "rappdirs", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "sessioninfo", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "testit", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" } ], "_owner": "richelbilderbeek", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "richelbilderbeek", "count": 4, "uuid": 2098230 }, { "user": "olivroy", "count": 2, "uuid": 52606734 } ], "_userbio": { "uuid": 2098230, "type": "user", "name": "Richèl Bilderbeek", "description": "Thinks Open Science is a pleonasm.\r\nIn my free time, I teach programming and lead programming teams, both for/with kids and adults." }, "_downloads": { "count": 224, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/netmhc2pan" }, "_devurl": "https://github.com/richelbilderbeek/netmhc2pan", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/netmhc2pan.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/richelbilderbeek/netmhc2pan", "_realowner": "richelbilderbeek", "_cranurl": true, "_releases": [ { "version": "1.3.1", "date": "2020-11-18" }, { "version": "1.3.2", "date": "2023-11-09" } ], "_exports": [ "capitalize_first_char", "check_alleles", "check_can_create_file", "check_fasta_file_sequence_lengths", "check_netmhc2pan_bin_url", "check_netmhc2pan_data_url", "check_netmhc2pan_installation", "create_temp_fasta_filename", "create_temp_xls_filename", "download_netmhc2pan_bin", "get_default_netmhc2pan_bin_path", "get_default_netmhc2pan_bin_tarfile_path", "get_default_netmhc2pan_folder", "get_default_netmhc2pan_subfolder", "get_default_netmhc2pan_version", "get_netmhc2pan_alleles", "get_netmhc2pan_archive_filename", "get_netmhc2pan_bin_url", "get_netmhc2pan_data_url", "get_netmhc2pan_url", "install_netmhc2pan", "install_netmhc2pan_bin", "install_netmhc2pan_bin_from_file", "install_netmhc2pan_data", "install_netmhc2pan_data_from_file", "install_netmhc2pan_from_files", "is_netmhc2pan_bin_installed", "is_netmhc2pan_data_installed", "is_netmhc2pan_haplotype", "is_netmhc2pan_installed", "is_netmhc2pan_set_up", "is_on_appveyor", "is_on_ci", "is_on_github_actions", "is_on_travis", "is_tcsh_installed", "is_url_valid", "netmhc2pan_report", "netmhc2pan_self_test", "predict_ic50", "predict_ic50s", "read_netmhc2pan_xls_output", "run_netmhc2pan", "set_up_netmhc2pan", "to_netmhc2pan_name", "uninstall_netmhc2pan" ], "_help": [ { "page": "capitalize_first_char", "title": "Convert the first character to upper case.", "topics": [ "capitalize_first_char" ] }, { "page": "check_alleles", "title": "Check the allele names", "topics": [ "check_alleles" ] }, { "page": "check_can_create_file", "title": "Check that a file can be created at a certain path.", "topics": [ "check_can_create_file" ] }, { "page": "check_fasta_file_sequence_lengths", "title": "Check the lengths of the sequences in a FASTA file", "topics": [ "check_fasta_file_sequence_lengths" ] }, { "page": "check_netmhc2pan_bin_url", "title": "Check the URL of the NetMHCIIpan binary tarball", "topics": [ "check_netmhc2pan_bin_url" ] }, { "page": "check_netmhc2pan_data_url", "title": "Check the URL of the NetMHCIIpan binary tarball", "topics": [ "check_netmhc2pan_data_url" ] }, { "page": "check_netmhc2pan_installation", "title": "Checks the installation of NetMHCIIpan.", "topics": [ "check_netmhc2pan_installation" ] }, { "page": "create_temp_fasta_filename", "title": "Create a '.fasta' file", "topics": [ "create_temp_fasta_filename" ] }, { "page": "create_temp_xls_filename", "title": "Create a '.xls' file", "topics": [ "create_temp_xls_filename" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit is parameters' documentation.", "topics": [ "default_params_doc" ] }, { "page": "download_netmhc2pan_bin", "title": "Download the NetMHCIIpan binary", "topics": [ "download_netmhc2pan_bin" ] }, { "page": "get_default_netmhc2pan_bin_path", "title": "Get the full path to the default NetMHC2pan binary", "topics": [ "get_default_netmhc2pan_bin_path" ] }, { "page": "get_default_netmhc2pan_bin_tarfile_path", "title": "Get the default path for the NetMHCIIpan binary tarball file", "topics": [ "get_default_netmhc2pan_bin_tarfile_path" ] }, { "page": "get_default_netmhc2pan_folder", "title": "Get the path to the folder where this package installs NetMHCIIpan by default", "topics": [ "get_default_netmhc2pan_folder" ] }, { "page": "get_default_netmhc2pan_subfolder", "title": "Get the full path to the NetMHC2pan sub-folder", "topics": [ "get_default_netmhc2pan_subfolder" ] }, { "page": "get_default_netmhc2pan_version", "title": "Get the default NetMHC2pan version used", "topics": [ "get_default_netmhc2pan_version" ] }, { "page": "get_netmhc2pan_alleles", "title": "Get a list of the alleles supported by NetMHCIIpan", "topics": [ "get_netmhc2pan_alleles" ] }, { "page": "get_netmhc2pan_archive_filename", "title": "Get the filename of the NetMHC2pan archive file", "topics": [ "get_netmhc2pan_archive_filename" ] }, { "page": "get_netmhc2pan_bin_url", "title": "Get the NetMHCIIpan binary download URL.", "topics": [ "get_netmhc2pan_bin_url" ] }, { "page": "get_netmhc2pan_data_url", "title": "Get the NetMHCIIpan data tarball URL.", "topics": [ "get_netmhc2pan_data_url" ] }, { "page": "get_netmhc2pan_url", "title": "Deprecated, use get_netmhc2pan_bin_url instead", "topics": [ "get_netmhc2pan_url" ] }, { "page": "install_netmhc2pan", "title": "Install NetMHCIIpan", "topics": [ "install_netmhc2pan" ] }, { "page": "install_netmhc2pan_bin", "title": "Install the NetMHCIIpan binary to a local folder", "topics": [ "install_netmhc2pan_bin" ] }, { "page": "install_netmhc2pan_bin_from_file", "title": "Install the NetMHCIIpan binary to a local folder", "topics": [ "install_netmhc2pan_bin_from_file" ] }, { "page": "install_netmhc2pan_data", "title": "Install the NetMHCIIpan data to a local folder", "topics": [ "install_netmhc2pan_data" ] }, { "page": "install_netmhc2pan_data_from_file", "title": "Install the NetMHCIIpan data from file", "topics": [ "install_netmhc2pan_data_from_file" ] }, { "page": "install_netmhc2pan_from_files", "title": "Install NetMHCIIpan from files.", "topics": [ "install_netmhc2pan_from_files" ] }, { "page": "is_netmhc2pan_bin_installed", "title": "Measure if NetMHCIIpan binary is installed locally", "topics": [ "is_netmhc2pan_bin_installed" ] }, { "page": "is_netmhc2pan_data_installed", "title": "Measure if NetMHCIIpan data folder is installed locally", "topics": [ "is_netmhc2pan_data_installed" ] }, { "page": "is_netmhc2pan_haplotype", "title": "Is the haplotype valid?", "topics": [ "is_netmhc2pan_haplotype" ] }, { "page": "is_netmhc2pan_installed", "title": "Measure if NetMHCIIpan is installed locally", "topics": [ "is_netmhc2pan_installed" ] }, { "page": "is_netmhc2pan_set_up", "title": "Measure if NetMHCIIpan is set up", "topics": [ "is_netmhc2pan_set_up" ] }, { "page": "is_on_appveyor", "title": "Determines if the environment is AppVeyor", "topics": [ "is_on_appveyor" ] }, { "page": "is_on_ci", "title": "Determines if the environment is a continuous integration service", "topics": [ "is_on_ci" ] }, { "page": "is_on_github_actions", "title": "Determines if the environment is GitHub Actions", "topics": [ "is_on_github_actions" ] }, { "page": "is_on_travis", "title": "Determines if the environment is Travis CI", "topics": [ "is_on_travis" ] }, { "page": "is_tcsh_installed", "title": "See if tcsh is installed", "topics": [ "is_tcsh_installed" ] }, { "page": "is_url_valid", "title": "Is the download URL valid?", "topics": [ "is_url_valid" ] }, { "page": "netmhc2pan", "title": "netmhc2pan: predict peptide binding strengths using NetMHC2pan", "topics": [ "netmhc2pan" ] }, { "page": "netmhc2pan_report", "title": "Show a 'netmhc2pan' report using message, to be used when reporting bugs", "topics": [ "netmhc2pan_report" ] }, { "page": "netmhc2pan_self_test", "title": "Test NetMHCIIpan by doing a minimal run.", "topics": [ "netmhc2pan_self_test" ] }, { "page": "predict_ic50", "title": "Predict the IC50 for peptides.", "topics": [ "predict_ic50" ] }, { "page": "predict_ic50s", "title": "Predict the IC50s from a sequence", "topics": [ "predict_ic50s" ] }, { "page": "read_netmhc2pan_xls_output", "title": "Read MHC2pan output", "topics": [ "read_netmhc2pan_xls_output" ] }, { "page": "run_netmhc2pan", "title": "Run NetMHCIIpan", "topics": [ "run_netmhc2pan" ] }, { "page": "set_up_netmhc2pan", "title": "Install the NetMHCIIpan binary to a local folder", "topics": [ "set_up_netmhc2pan" ] }, { "page": "to_netmhc2pan_name", "title": "Convert a formal haplotype name to its NetMHC2pan notation", "topics": [ "to_netmhc2pan_name" ] }, { "page": "uninstall_netmhc2pan", "title": "Uninstall NetMHCIIpan", "topics": [ "uninstall_netmhc2pan" ] } ], "_readme": "https://github.com/richelbilderbeek/netmhc2pan/raw/HEAD/README.md", "_rundeps": [ "ade4", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "dplyr", "generics", "glue", "hms", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pillar", "pixmap", "pkgconfig", "prettyunits", "progress", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "readr", "rlang", "segmented", "seqinr", "sessioninfo", "sp", "stringi", "stringr", "testit", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "demo.Rmd", "filename": "demo.html", "title": "Binding strength prediction", "author": "Richel J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [], "created": "2018-12-28 07:38:38", "modified": "2023-11-07 12:11:27", "commits": 16 } ], "_score": 4, "_indexed": true, "_nocasepkg": "netmhc2pan", "_universes": [ "richelbilderbeek" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.3", "date": "2026-05-12T06:34:53.000Z", "distro": "noble", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "8d63e7c69064b55703b0ff4dd654f8ac26e1fa9700baa2908df0e8ecbd238353", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.6.0", "os": "linux", "version": "1.3.3", "date": "2026-05-12T06:34:48.000Z", "distro": "noble", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "2cde05a57f23c78729b4b43a8020b8b4094962c859f1695db9a771b239fccfb5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.5.3", "os": "mac", "version": "1.3.3", "date": "2026-05-12T06:34:22.000Z", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "5417c6ab728e5c14b611df170c1f0c2eb6189e3ebd463eff372646960a35e56a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.6.0", "os": "mac", "version": "1.3.3", "date": "2026-05-12T06:34:12.000Z", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "f42b94b15a0667a1507979712f2696a624b189d1abfca10b1a6a88f7bc21f4e5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.7.0", "os": "win", "version": "1.3.3", "date": "2026-05-12T06:34:11.000Z", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "93fe03326cfd7005393f07ef6b43fb0a510aded0622843cb5d11728635ef1c0a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.5.3", "os": "win", "version": "1.3.3", "date": "2026-05-12T06:33:59.000Z", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "b7d7249e4eb0a8e7c9746ed0bfe5a352533bb8e6d54fa5cfe96b7932eb3641f5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.6.0", "os": "win", "version": "1.3.3", "date": "2026-05-12T06:33:48.000Z", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "ab5a2852da9cfba19b3ef373d1a8ae561ea00eb65eca0376b45c0f123c833a24", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.3", "date": "2026-05-22T10:59:29.000Z", "commit": "620be78c23c60b72809fe6ff4fdf13012e8076a5", "fileid": "cc15f0e68e8cd0e1e8e3f44fa75f2287f2a64cd2f7157059130e22dbfeec3e1d", "status": "success", "buildurl": "https://github.com/r-universe/richelbilderbeek/actions/runs/25717575922" } ] }