Package: mhcnuggetsr 1.2.2

mhcnuggetsr: Call MHCnuggets

MHCnuggets (<https://github.com/KarchinLab/mhcnuggets>) is a Python tool to predict MHC class I and MHC class II epitopes. This package allows one to call MHCnuggets from R.

Authors:Richèl J.C. Bilderbeek [aut, cre], Joshua van Waardenberg [ctb]

mhcnuggetsr_1.2.2.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mhcnuggetsr/json (API)

# Install 'mhcnuggetsr' in R:

install.packages('mhcnuggetsr', repos = c('https://richelbilderbeek.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/richelbilderbeek/mhcnuggetsr/issues

On CRAN:

4.48 score 4 stars 15 scripts 233 downloads 51 exports 103 dependencies

Last updated from:6161af6649. Checks:4 NOTE, 2 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	172
source / vignettes	OK	282
linux-release-x86_64	NOTE	230
macos-release-arm64	NOTE	123
macos-oldrel-arm64	NOTE	137
windows-devel	ERROR	144
windows-release	ERROR	142
windows-oldrel	ERROR	206
wasm-release	OK	195

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

Dependencies: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 RcppTOML reticulate rlang rmarkdown roxygen2 rprojroot rstudioapi rversions sass sessioninfo shiny sourcetools stringi stringr sys systemfonts testthat textshaping tibble tidyselect tinytex urlchecker usethis utf8 vctrs waldo whisker withr xfun xml2 xopen xtable yaml zip

demo

Appendix | All example files | All MHC-I haplotypes | All MHC-II haplotypes | Session info

Rendered fromdemo.Rmdusingknitr::rmarkdown

Last update: 2021-07-30
Started: 2020-05-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Are these MHCnuggets names?	are_mhcnuggets_names
Check the 'ba_models'	check_ba_models
Check if a file exists.	check_file_exists
Check if 'mhc' is a valud MHCnuggets name	check_mhc
Check the MHC class.	check_mhc_class
Check if MHCnuggets is installed.	check_mhcnuggets_installation
Check the MHCnuggets options.	check_mhcnuggets_options
Check the names of the elements in an 'mhcnuggets_options' list.	check_mhcnuggets_options_names
Check the 'mhcnuggets_url'	check_mhcnuggets_url
Check the 'mhcnuggetsr_folder'	check_mhcnuggetsr_folder
Check the 'verbose'	check_verbose
Create a set of MHCnuggets options.	create_mhcnuggets_options
Create a path to a non-existing temporary file	create_temp_peptides_path
Create testing options for MHCnuggets	create_test_mhcnuggets_options
This function does nothing. It is intended to inherit the documentation of the parameters from.	default_params_doc
Downgrade pip.	downgrade_pip
Get the path to the folder where this package installs 'MHCnuggets' by default	get_default_mhcnuggets_folder
Get the path to the folder where this package installs the required Python packages by default	get_default_mhcnuggetsr_folder
Get the default folder for ormr.	get_default_orm_folder_name
Get the default 'ormr' folder name	get_default_ormr_folder_name
Get the default version of Python used	get_default_python_version
Get the full path to an MHCnuggets example file	get_example_filename
Get the full path to all MHCnuggets example files	get_example_filenames
Get all the MHC-I haplotypes	get_mhc_1_haplotypes
Get all the MHC-II haplotypes	get_mhc_2_haplotypes
Get the URL of the MHCnuggets source code	get_mhcnuggets_url
Get the MHCnuggets version	get_mhcnuggets_version
Get the version of all Python packages	get_python_package_versions
Get all the MHC-I haplotypes that have been trained on a model	get_trained_mhc_1_haplotypes
Get all the MHC-II haplotypes that have been trained on a model	get_trained_mhc_2_haplotypes
Install the 'MHCnuggets' 'Python' package.	install_mhcnuggets
Install pip.	install_pip
Check if MHCnuggets is installed	is_mhcnuggets_installed
Is this an MHCnuggets name?	is_mhcnuggets_name
Is this a 'mhcnuggets_options'?	is_mhcnuggets_options
Determines if the environment is AppVeyor	is_on_appveyor
Determines if the environment is a continuous integration service	is_on_ci
Determines if the environment is Travis CI	is_on_travis
Determine if pip is installed	is_pip_installed
Convert a 'mhcnuggets_options' to text	mhcnuggets_options_to_text
Create a mhcnuggetsr report, to be used when reporting bugs	mhcnuggetsr_report
Self-test the package	mhcnuggetsr_self_test
Predict the IC50 for peptides.	predict_ic50
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)	predict_ic50_from_file
Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide	predict_ic50s
Set the MHCnuggets installation state to the desired one	set_is_mhcnuggets_installed
Set the version of pip.	set_pip_version
Convert a standard haplotype name to the MHCnuggets name	to_mhcnuggets_name
Convert one or more standard haplotype name to the MHCnuggets names	to_mhcnuggets_names
Uninstall the MHCnuggets Python package.	uninstall_mhcnuggets
Install pip.	uninstall_pip
Uograde pip.	upgrade_pip