R: Call MHCnuggets

# Call MHCnuggets

## Documentation for package ‘mhcnuggetsr’ version 1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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