{ "_id": "6a4681f46ff6f2357554b993", "Package": "mhcnuggetsr", "Title": "Call MHCnuggets", "Version": "1.2.2", "Authors@R": "c(\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"rjcbilderbeek@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1107-7049\")),\nperson(\"Joshua\", \"van Waardenberg\", role = c(\"ctb\")))", "Maintainer": "Richèl J.C. Bilderbeek ", "Description": "MHCnuggets () is\na Python tool to predict MHC class I and MHC class II epitopes.\nThis package allows one to call MHCnuggets from R.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "URL": "https://github.com/richelbilderbeek/mhcnuggetsr/", "BugReports": "https://github.com/richelbilderbeek/mhcnuggetsr", "Language": "en-US", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev libgit2-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev python3 libx11-dev zlib1g-dev", "Repository": "https://richelbilderbeek.r-universe.dev", "Date/Publication": "2026-07-02 14:14:48 UTC", "RemoteUrl": "https://github.com/richelbilderbeek/mhcnuggetsr", "RemoteRef": "HEAD", "RemoteSha": "6161af6649c78f7bd47cbe7566d178e63e57b0e4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-02 15:16:49 UTC", "User": "root" }, "Author": "Richèl J.C. 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"_stars": 4, "_contributors": [ { "user": "richelbilderbeek", "count": 12, "uuid": 2098230 }, { "user": "dyncoder", "count": 3, "uuid": 29332370 } ], "_userbio": { "uuid": 2098230, "type": "user", "name": "Richèl Bilderbeek", "followers": 414, "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": 233, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mhcnuggetsr" }, "_devurl": "https://github.com/richelbilderbeek/mhcnuggetsr", "_searchresults": 15, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mhcnuggetsr.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/richelbilderbeek/mhcnuggetsr", "_realowner": "richelbilderbeek", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2020-11-04" } ], "_exports": [ "are_mhcnuggets_names", "check_ba_models", "check_file_exists", "check_mhc", "check_mhc_class", "check_mhcnuggets_installation", "check_mhcnuggets_options", "check_mhcnuggets_options_names", "check_mhcnuggets_url", "check_mhcnuggetsr_folder", "check_verbose", "create_mhcnuggets_options", "create_temp_peptides_path", "create_test_mhcnuggets_options", "downgrade_pip", "get_default_mhcnuggets_folder", "get_default_mhcnuggetsr_folder", "get_default_orm_folder_name", "get_default_ormr_folder_name", "get_default_python_version", "get_example_filename", "get_example_filenames", "get_mhc_1_haplotypes", "get_mhc_2_haplotypes", "get_mhcnuggets_url", "get_mhcnuggets_version", "get_python_package_versions", "get_trained_mhc_1_haplotypes", "get_trained_mhc_2_haplotypes", "install_mhcnuggets", "install_pip", "is_mhcnuggets_installed", "is_mhcnuggets_name", "is_mhcnuggets_options", "is_on_appveyor", "is_on_ci", "is_on_travis", "is_pip_installed", "mhcnuggets_options_to_text", "mhcnuggetsr_report", "mhcnuggetsr_self_test", "predict_ic50", "predict_ic50_from_file", "predict_ic50s", "set_is_mhcnuggets_installed", "set_pip_version", "to_mhcnuggets_name", "to_mhcnuggets_names", "uninstall_mhcnuggets", "uninstall_pip", "upgrade_pip" ], "_help": [ { "page": "are_mhcnuggets_names", "title": "Are these MHCnuggets names?", "topics": [ "are_mhcnuggets_names" ] }, { "page": "check_ba_models", "title": "Check the 'ba_models'", "topics": [ "check_ba_models" ] }, { "page": "check_file_exists", "title": "Check if a file exists.", "topics": [ "check_file_exists" ] }, { "page": "check_mhc", "title": "Check if 'mhc' is a valud MHCnuggets name", "topics": [ "check_mhc" ] }, { "page": "check_mhc_class", "title": "Check the MHC class.", "topics": [ "check_mhc_class" ] }, { "page": "check_mhcnuggets_installation", "title": "Check if MHCnuggets is installed.", "topics": [ "check_mhcnuggets_installation" ] }, { "page": "check_mhcnuggets_options", "title": "Check the MHCnuggets options.", "topics": [ "check_mhcnuggets_options" ] }, { "page": "check_mhcnuggets_options_names", "title": "Check the names of the elements in an 'mhcnuggets_options' list.", "topics": [ "check_mhcnuggets_options_names" ] }, { "page": "check_mhcnuggets_url", "title": "Check the 'mhcnuggets_url'", "topics": [ "check_mhcnuggets_url" ] }, { "page": "check_mhcnuggetsr_folder", "title": "Check the 'mhcnuggetsr_folder'", "topics": [ "check_mhcnuggetsr_folder" ] }, { "page": "check_verbose", "title": "Check the 'verbose'", "topics": [ "check_verbose" ] }, { "page": "create_mhcnuggets_options", "title": "Create a set of MHCnuggets options.", "topics": [ "create_mhcnuggets_options" ] }, { "page": "create_temp_peptides_path", "title": "Create a path to a non-existing temporary file", "topics": [ "create_temp_peptides_path" ] }, { "page": "create_test_mhcnuggets_options", "title": "Create testing options for MHCnuggets", "topics": [ "create_test_mhcnuggets_options" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit the documentation of the parameters from.", "topics": [ "default_params_doc" ] }, { "page": "downgrade_pip", "title": "Downgrade pip.", "topics": [ "downgrade_pip" ] }, { "page": "get_default_mhcnuggets_folder", "title": "Get the path to the folder where this package installs 'MHCnuggets' by default", "topics": [ "get_default_mhcnuggets_folder" ] }, { "page": "get_default_mhcnuggetsr_folder", "title": "Get the path to the folder where this package installs the required Python packages by default", "topics": [ "get_default_mhcnuggetsr_folder" ] }, { "page": "get_default_orm_folder_name", "title": "Get the default folder for ormr.", "topics": [ "get_default_orm_folder_name" ] }, { "page": "get_default_ormr_folder_name", "title": "Get the default 'ormr' folder name", "topics": [ "get_default_ormr_folder_name" ] }, { "page": "get_default_python_version", "title": "Get the default version of Python used", "topics": [ "get_default_python_version" ] }, { "page": "get_example_filename", "title": "Get the full path to an MHCnuggets example file", "topics": [ "get_example_filename" ] }, { "page": "get_example_filenames", "title": "Get the full path to all MHCnuggets example files", "topics": [ "get_example_filenames" ] }, { "page": "get_mhc_1_haplotypes", "title": "Get all the MHC-I haplotypes", "topics": [ "get_mhc_1_haplotypes" ] }, { "page": "get_mhc_2_haplotypes", "title": "Get all the MHC-II haplotypes", "topics": [ "get_mhc_2_haplotypes" ] }, { "page": "get_mhcnuggets_url", "title": "Get the URL of the MHCnuggets source code", "topics": [ "get_mhcnuggets_url" ] }, { "page": "get_mhcnuggets_version", "title": "Get the MHCnuggets version", "topics": [ "get_mhcnuggets_version" ] }, { "page": "get_python_package_versions", "title": "Get the version of all Python packages", "topics": [ "get_python_package_versions" ] }, { "page": "get_trained_mhc_1_haplotypes", "title": "Get all the MHC-I haplotypes that have been trained on a model", "topics": [ "get_trained_mhc_1_haplotypes" ] }, { "page": "get_trained_mhc_2_haplotypes", "title": "Get all the MHC-II haplotypes that have been trained on a model", "topics": [ "get_trained_mhc_2_haplotypes" ] }, { "page": "install_mhcnuggets", "title": "Install the 'MHCnuggets' 'Python' package.", "topics": [ "install_mhcnuggets" ] }, { "page": "install_pip", "title": "Install pip.", "topics": [ "install_pip" ] }, { "page": "is_mhcnuggets_installed", "title": "Check if MHCnuggets is installed", "topics": [ "is_mhcnuggets_installed" ] }, { "page": "is_mhcnuggets_name", "title": "Is this an MHCnuggets name?", "topics": [ "is_mhcnuggets_name" ] }, { "page": "is_mhcnuggets_options", "title": "Is this a 'mhcnuggets_options'?", "topics": [ "is_mhcnuggets_options" ] }, { "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_travis", "title": "Determines if the environment is Travis CI", "topics": [ "is_on_travis" ] }, { "page": "is_pip_installed", "title": "Determine if pip is installed", "topics": [ "is_pip_installed" ] }, { "page": "mhcnuggets_options_to_text", "title": "Convert a 'mhcnuggets_options' to text", "topics": [ "mhcnuggets_options_to_text" ] }, { "page": "mhcnuggetsr_report", "title": "Create a mhcnuggetsr report, to be used when reporting bugs", "topics": [ "mhcnuggetsr_report" ] }, { "page": "mhcnuggetsr_self_test", "title": "Self-test the package", "topics": [ "mhcnuggetsr_self_test" ] }, { "page": "predict_ic50", "title": "Predict the IC50 for peptides.", "topics": [ "predict_ic50" ] }, { "page": "predict_ic50_from_file", "title": "Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides as saved in a file. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)", "topics": [ "predict_ic50_from_file" ] }, { "page": "predict_ic50s", "title": "Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide", "topics": [ "predict_ic50s" ] }, { "page": "set_is_mhcnuggets_installed", "title": "Set the MHCnuggets installation state to the desired one", "topics": [ "set_is_mhcnuggets_installed" ] }, { "page": "set_pip_version", "title": "Set the version of pip.", "topics": [ "set_pip_version" ] }, { "page": "to_mhcnuggets_name", "title": "Convert a standard haplotype name to the MHCnuggets name", "topics": [ "to_mhcnuggets_name" ] }, { "page": "to_mhcnuggets_names", "title": "Convert one or more standard haplotype name to the MHCnuggets names", "topics": [ "to_mhcnuggets_names" ] }, { "page": "uninstall_mhcnuggets", "title": "Uninstall the MHCnuggets Python package.", "topics": [ "uninstall_mhcnuggets" ] }, { "page": "uninstall_pip", "title": "Install pip.", "topics": [ "uninstall_pip" ] }, { "page": "upgrade_pip", "title": "Uograde pip.", "topics": [ "upgrade_pip" ] } ], "_readme": "https://github.com/richelbilderbeek/mhcnuggetsr/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "brew", "brio", "bslib", "cachem", "callr", "cli", "clipr", "commonmark", "cpp11", "crayon", "credentials", "curl", "desc", "devtools", "diffobj", "digest", "downlit", "dplyr", "ellipsis", "evaluate", "fansi", "fastmap", "fontawesome", "fs", "generics", "gert", "gitcreds", "glue", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr2", "ini", "jquerylib", "jsonlite", "knitr", "later", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "miniUI", "openssl", "otel", "pak", "pillar", "pkgbuild", "pkgconfig", "pkgdown", "pkgload", "png", "praise", "prettyunits", "processx", "profvis", "promises", "ps", "purrr", "R6", "ragg", "rappdirs", "rcmdcheck", "Rcpp", 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